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CHEMISTRY (598 journals)                  1 2 3 | Last

Showing 1 - 200 of 735 Journals sorted alphabetically
2D Materials     Hybrid Journal   (Followers: 10)
Accreditation and Quality Assurance: Journal for Quality, Comparability and Reliability in Chemical Measurement     Hybrid Journal   (Followers: 26)
ACS Catalysis     Full-text available via subscription   (Followers: 38)
ACS Chemical Neuroscience     Full-text available via subscription   (Followers: 18)
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Acta Chemica Iasi     Open Access   (Followers: 2)
Acta Chimica Sinica     Full-text available via subscription   (Followers: 1)
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Acta Chromatographica     Full-text available via subscription   (Followers: 9)
Acta Facultatis Medicae Naissensis     Open Access  
Acta Metallurgica Sinica (English Letters)     Hybrid Journal   (Followers: 5)
Acta Scientifica Naturalis     Open Access   (Followers: 2)
adhäsion KLEBEN & DICHTEN     Hybrid Journal   (Followers: 5)
Adhesion Adhesives & Sealants     Hybrid Journal   (Followers: 8)
Adsorption Science & Technology     Full-text available via subscription   (Followers: 5)
Advanced Functional Materials     Hybrid Journal   (Followers: 51)
Advanced Science Focus     Free   (Followers: 3)
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Advances in Quantum Chemistry     Full-text available via subscription   (Followers: 5)
Advances in Science and Technology     Full-text available via subscription   (Followers: 12)
African Journal of Bacteriology Research     Open Access  
African Journal of Chemical Education     Open Access   (Followers: 2)
African Journal of Pure and Applied Chemistry     Open Access   (Followers: 7)
Agrokémia és Talajtan     Full-text available via subscription   (Followers: 2)
Al-Kimia : Jurnal Penelitian Sains Kimia     Open Access  
Alkaloids: Chemical and Biological Perspectives     Full-text available via subscription   (Followers: 3)
AMB Express     Open Access   (Followers: 1)
Ambix     Hybrid Journal   (Followers: 3)
American Journal of Biochemistry and Biotechnology     Open Access   (Followers: 66)
American Journal of Biochemistry and Molecular Biology     Open Access   (Followers: 15)
American Journal of Chemistry     Open Access   (Followers: 27)
American Journal of Plant Physiology     Open Access   (Followers: 14)
American Mineralogist     Hybrid Journal   (Followers: 14)
Analyst     Full-text available via subscription   (Followers: 39)
Angewandte Chemie     Hybrid Journal   (Followers: 179)
Angewandte Chemie International Edition     Hybrid Journal   (Followers: 231)
Annales UMCS, Chemia     Open Access   (Followers: 1)
Annals of Clinical Chemistry and Laboratory Medicine     Open Access   (Followers: 4)
Annual Reports in Computational Chemistry     Full-text available via subscription   (Followers: 3)
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Annual Review of Chemical and Biomolecular Engineering     Full-text available via subscription   (Followers: 12)
Annual Review of Food Science and Technology     Full-text available via subscription   (Followers: 16)
Anti-Infective Agents     Hybrid Journal   (Followers: 3)
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Applied Organometallic Chemistry     Hybrid Journal   (Followers: 7)
Applied Spectroscopy     Full-text available via subscription   (Followers: 22)
Applied Surface Science     Hybrid Journal   (Followers: 28)
Arabian Journal of Chemistry     Open Access   (Followers: 6)
ARKIVOC     Open Access   (Followers: 2)
Asian Journal of Biochemistry     Open Access   (Followers: 1)
Atomization and Sprays     Full-text available via subscription   (Followers: 4)
Australian Journal of Chemistry     Hybrid Journal   (Followers: 7)
Autophagy     Hybrid Journal   (Followers: 2)
Avances en Quimica     Open Access   (Followers: 1)
Biochemical Pharmacology     Hybrid Journal   (Followers: 10)
Biochemistry     Full-text available via subscription   (Followers: 324)
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Bioinorganic Chemistry and Applications     Open Access   (Followers: 9)
Bioinspired Materials     Open Access   (Followers: 5)
Biointerface Research in Applied Chemistry     Open Access   (Followers: 2)
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Biomacromolecules     Full-text available via subscription   (Followers: 19)
Biomass Conversion and Biorefinery     Partially Free   (Followers: 10)
Biomedical Chromatography     Hybrid Journal   (Followers: 6)
Biomolecular NMR Assignments     Hybrid Journal   (Followers: 3)
BioNanoScience     Partially Free   (Followers: 5)
Bioorganic & Medicinal Chemistry     Hybrid Journal   (Followers: 120)
Bioorganic & Medicinal Chemistry Letters     Hybrid Journal   (Followers: 84)
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Bitácora Digital     Open Access  
Boletin de la Sociedad Chilena de Quimica     Open Access  
Bulletin of the Chemical Society of Ethiopia     Open Access   (Followers: 2)
Bulletin of the Chemical Society of Japan     Full-text available via subscription   (Followers: 24)
Bulletin of the Korean Chemical Society     Hybrid Journal   (Followers: 1)
C - Journal of Carbon Research     Open Access   (Followers: 3)
Cakra Kimia (Indonesian E-Journal of Applied Chemistry)     Open Access  
Canadian Association of Radiologists Journal     Full-text available via subscription   (Followers: 3)
Canadian Journal of Chemistry     Hybrid Journal   (Followers: 10)
Canadian Mineralogist     Full-text available via subscription   (Followers: 5)
Carbohydrate Research     Hybrid Journal   (Followers: 26)
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Catalysis for Sustainable Energy     Open Access   (Followers: 7)
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Catalysis Science and Technology     Free   (Followers: 7)
Catalysis Surveys from Asia     Hybrid Journal   (Followers: 3)
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Chemical Bulletin of Kazakh National University     Open Access  
Chemical Communications     Full-text available via subscription   (Followers: 70)
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Chemical Research in Chinese Universities     Hybrid Journal   (Followers: 3)
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Chemical Reviews     Full-text available via subscription   (Followers: 185)
Chemical Science     Open Access   (Followers: 22)
Chemical Technology     Open Access   (Followers: 16)
Chemical Vapor Deposition     Hybrid Journal   (Followers: 5)
Chemical Week     Full-text available via subscription   (Followers: 8)
Chemie in Unserer Zeit     Hybrid Journal   (Followers: 56)
Chemie-Ingenieur-Technik (Cit)     Hybrid Journal   (Followers: 24)
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Chemistry & Industry     Hybrid Journal   (Followers: 5)
Chemistry - A European Journal     Hybrid Journal   (Followers: 147)
Chemistry - An Asian Journal     Hybrid Journal   (Followers: 15)
Chemistry and Materials Research     Open Access   (Followers: 20)
Chemistry Central Journal     Open Access   (Followers: 4)
Chemistry Education Research and Practice     Free   (Followers: 5)
Chemistry in Education     Open Access   (Followers: 9)
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Chemistry Letters     Full-text available via subscription   (Followers: 42)
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Chemistry of Natural Compounds     Hybrid Journal   (Followers: 9)
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ChemistryOpen     Open Access   (Followers: 2)
Chemkon - Chemie Konkret, Forum Fuer Unterricht Und Didaktik     Hybrid Journal  
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Chemosensors     Open Access  
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ChemTexts     Hybrid Journal  
CHIMIA International Journal for Chemistry     Full-text available via subscription   (Followers: 2)
Chinese Journal of Chemistry     Hybrid Journal   (Followers: 6)
Chinese Journal of Polymer Science     Hybrid Journal   (Followers: 10)
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Clay Minerals     Full-text available via subscription   (Followers: 10)
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Colloids and Surfaces B: Biointerfaces     Hybrid Journal   (Followers: 6)
Combinatorial Chemistry & High Throughput Screening     Hybrid Journal   (Followers: 4)
Combustion Science and Technology     Hybrid Journal   (Followers: 19)
Comments on Inorganic Chemistry: A Journal of Critical Discussion of the Current Literature     Hybrid Journal   (Followers: 2)
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        1 2 3 | Last

Journal Cover Biomolecular NMR Assignments
  [SJR: 0.325]   [H-I: 10]   [3 followers]  Follow
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 1874-2718 - ISSN (Online) 1874-270X
   Published by Springer-Verlag Homepage  [2355 journals]
  • 1 H, 13 C and 15 N backbone and partial side-chain resonance assignments
           of the C-terminal domain of HIV-1 Pr55 Gag encompassed in NCp15
    • Authors: Valéry Larue; Marjorie Catala; Anissa Belfetmi; Loussiné Zargarian; Olivier Mauffret; Carine Tisné
      Abstract: Abstract During HIV-1 assembly, the Pr55Gag polyprotein precursor (Gag) interacts with the genomic RNA, with lipids of the plasma membrane, with host proteins (ALIX, TSG101) through the ESCRT complex, with the viral protein Vpr and are involved in intermolecular interactions with other Pr55Gag proteins. This network of interactions is responsible for the formation of the viral particle, the selection of genomic RNA and the packaging of Vpr. The C-terminal domain of Gag encompassed in NCp15 is involved in the majority of these interactions, either by its nucleocapsid or its p6 domains. We study the NCp15 protein as a model of the C-terminal domain of Gag to better understand the role of this domain in the assembly and budding of HIV-1. Here, we report the 1H, 13C and 15N chemical shift assignments of NCp15 obtained by heteronuclear multidimensional NMR spectroscopy as well as the analysis of its secondary structure in solution. These assignments of NCp15 pave the way for interaction studies with its numerous partners.
      PubDate: 2018-01-13
      DOI: 10.1007/s12104-017-9796-x
  • Chemical shift assignments of retinal degeneration 3 protein (RD3)
    • Authors: Sunghyuk Lim; Diana Cudia; Qinhong Yu; Igor Peshenko; Alexander M. Dizhoor; James B. Ames
      Abstract: Abstract Retinal degeneration 3 protein (RD3) binds to retinal membrane guanylyl cyclase (RetGC) and suppresses the basal activity of RetGC in photoreceptor cells that opposes the allosteric activation of the cyclase by GCAP proteins. Mutations in RD3 that disrupt its inhibition of RetGC are implicated in human retinal degenerative disorders. Here we report both backbone and sidechain NMR assignments for the RD3 protein (BMRB accession no. 27305).
      PubDate: 2018-01-11
      DOI: 10.1007/s12104-018-9802-y
  • 1 H, 13 C and 15 N resonance assignments of NEDD8 from Trypanosoma brucei
    • Authors: Rui Wang; Jiahai Zhang; Shanhui Liao; Xiaoming Tu
      Abstract: Abstract Neural precursor cell-expressed, developmently downregulated 8 (NEDD8) is a small ubiquitin-like modifier, which plays important roles in many cellular processes. Although it has been well studied in many eukaryotes, NEDD8 is still uncharacterized in some unicellular parasites, such as Trypanosoma brucei (T. brucei). Here we report the resonance assignments of NEDD8 from T. brucei.
      PubDate: 2018-01-11
      DOI: 10.1007/s12104-018-9800-0
  • Chemical shift assignments of CHU_1110: an AHSA1-like protein from
           Cytophaga hutchinsonii
    • Authors: Chunjie Liang; Ting He; Tao Li; Yunhuang Yang; Jiang Zhu; Maili Liu
      Abstract: Abstract AHSA1 protein family is one of the four largest families in the Bet v1-like protein superfamily. The functions and structures of proteins in AHSA1 family are still largely unknown. CHU_1110 with 167 amino acids and a molecular weight of 19.2 kDa is a member of the AHSA1 family from Cytophaga hutchinsonii, a soil bacterium known for its ability to digest crystalline cellulose. Here we report the complete 1H, 13C and 15N chemical shift assignments of CHU_1110. The secondary structural elements of CGL2373 are consistent with the canonical AHSA1 structure. However the sequence identity of CHU_1110 with other members of AHSA1 family with functional and structural reports, such as RHE_CH02687 from Rhizobium etli, Aha1 from Homo sapiens and Yndb from Bacillus subtilis, are very low, which may suggest a different function of CHU_1110. Our chemical shift assignments of CHU_1110 are essential for the following structural and functional research of CHU_1110.
      PubDate: 2018-01-09
      DOI: 10.1007/s12104-018-9799-2
  • Backbone and side-chain chemical shift assignments of the kringle domain
           of human receptor tyrosine kinase-like orphan receptor 1 (ROR1)
    • Authors: Xiaofang Ma; Yingying Zhang; Bin Liu; Jiahui Yang; Kaifeng Hu
      Abstract: Abstract Receptor tyrosine kinase-like orphan receptor 1 (ROR1) expresses at high level in many cancers and has been suggested as a potential therapeutic target. It was reported that the Kringle (KNG) domain of ROR1 extracellular region is involved in ROR1/ROR2 heterooligomerization. Monoantibodies that target KNG domain of ROR1 could induce apoptosis of chronic lymphocytic leukemia cells. Here we present the backbone and side chain assignments of KNG domain of ROR1, which lays a foundation for its further structural and function research.
      PubDate: 2018-01-08
      DOI: 10.1007/s12104-017-9797-9
  • Backbone resonance assignment of the response regulator protein PhoB N
           F20D from Escherichia coli
    • Authors: Xinhui Kou; Xinghong Liu; Yixiang Liu; Conggang Li; Maili Liu; Ling Jiang
      Abstract: Abstract PhoB is a response regulator of the PhoR/PhoB two-component signal transduction system that is involved in the regulation of the phosphate (Pho) regulon of Escherichia coli. PhoB has two domains, receiver domain and effector domain. The receiver domain can be phosphorylated by its cognate histidine kinase PhoR and the phosphorylation induces conformational changes of the full length protein of PhoB that promote the DNA binding and transcription. Three-dimensional crystal structures of PhoB receiver domain (PhoBN) have been solved under apo or BeF3− (a phosphoryl analog) binding forms and it has been found that PhoBN is dimerized in both situations. However, we have found that the apo form of PhoBN has multiple conformational changes in solution that is hard to be distinguished by using NMR spectroscopy, while the mutagenesis of F20D PhoBN gives homogeneous dispersed signals in HSQC spectrum indicating a relatively uniform conformation. Meanwhile the F20D mutant has the same phosphorylation activity as the wild type protein. Here we report the backbone assignment of PhoBNF20D mutant. The chemical shift (HN, N, CO, Cα and Cβ) analysis shows that the predicted regions of secondary structure are in good agreement with those observed in the crystal structure of apo PhoBN. Therefore, the backbone chemical shifts assignment of PhoBNF20D mutant would be useful for studying the structure and dynamics of PhoB receiver domain and it has significance for explaining the mechanism of phosphorylation in TCSs.
      PubDate: 2018-01-03
      DOI: 10.1007/s12104-017-9795-y
  • 1 H, 13 C and 15 N NMR assignments of a bacterial immunoglobulin-like
           domain (group 2) of a protein of a bacterium Paenarthrobacter aurescens
    • Authors: Asmita D. Pawar; Deepshikha Verma; Rajeev Raman; Yogendra Sharma; Kandala V. R. Chary
      Pages: 203 - 206
      Abstract: Abstract The bacterial immunoglobulin-like (Big) domain is one of the prevalent domain types, which facilitates cell–cell adhesion by assembling into multi-domain architectures. We selected a four Big_2 domain protein (named ‘Arig’) from a Gram positive, Paenarthrobacter aurescens TC1 (known earlier as Arthrobacter aurescens TC1). In an attempt to characterize structural and ligand-binding features of individual Big_2 domains, we have cloned, overexpressed, isolated and purified the second Big_2 domain of Arig along with a few of its adjacent Big_2 domain residues (residue 143 to 269) referred to as ‘Arig2’. The 13C/15N-doubly-labeled His-tagged Arig2 (133 residues long) showed an ordered conformation as revealed by the well dispersed 2D [15N-1H]-HSQC spectrum. Subsequently, a suite of heteronuclear 3D NMR experiments has enabled almost complete 1H, 13C and 15N NMR resonance assignments of Arig2.
      PubDate: 2017-10-01
      DOI: 10.1007/s12104-017-9748-5
      Issue No: Vol. 11, No. 2 (2017)
  • Assignment of 1 H, 13 C and 15 N resonances and secondary structure of the
           Rgd1-RhoGAP domain
    • Authors: Denis Martinez; Valérie Prouzet-Mauléon; Michel Hugues; François Doignon; Benoît Odaert
      Abstract: Abstract The protein Rgd1 is involved in the regulation of cytoskeleton formation and in signalling pathways that control cell polarity and growth in Saccharomyces cerevisiae. Rgd1p is composed of a F-BAR domain required for membrane binding and a RhoGAP domain responsible for activating Rho3p and Rho4p, two GTPases respectively involved in bud growth and cytokinesis. Rgd1p is recruited to the membrane through interactions with phosphoinositide lipids, which bind the two isolated domains and stimulate the RhoGAP activity on Rho4p. As previously shown by crystallography, the membrane-binding F-BAR domain contains a conserved inositol phosphate binding site, which explains the preferential binding of phosphoinositides. In contrast, RhoGAP domains are not expected to bind lipids. In order to unravel this puzzling feature, we solved the three-dimensional structure of the isolated protein and found a cryptic phosphoinositide binding site involving non conserved residues (Martinez et al. 2017). The assignment of the resonances and secondary structure of Rgd1-RhoGAP (aa 450–666) is presented here.
      PubDate: 2017-12-26
      DOI: 10.1007/s12104-017-9794-z
  • Chemical shift assignments of the partially deuterated Fyn SH2–SH3
    • Authors: Fabien Kieken; Karine Loth; Nico van Nuland; Peter Tompa; Tom Lenaerts
      Abstract: Abstract Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1H, 15N and 13C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3–SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.
      PubDate: 2017-12-09
      DOI: 10.1007/s12104-017-9792-1
  • 1 H, 13 C, and 15 N chemical shift assignments of a G-quadruplex forming
           sequence within the KRAS proto-oncogene promoter region
    • Authors: Julien Marquevielle; M. V. Vasantha Kumar; Jean-Louis Mergny; Gilmar F. Salgado
      Abstract: Abstract Single stranded guanine rich DNA (or RNA) sequences adopt noncanonical secondary structures called G-quadruplexes (G4). Functionally, quadruplexes control gene transcription and regulate activities such as replication, gene recombination or alternative splicing. Hence they are potential targets for cancer, neuronal, and viral related diseases. KRAS is one of the most mutated oncogenes in the genome of cancer cells and contains a nuclease hypersensitive element (NHE) sequence capable of forming G-quadruplexes via its six runs of guanines. In our work, we are interested in the NMR structure of the major G4 scaffold formed in the KRAS NHE region with a mutated sequence of 22 residues. Here, we report 1H, 13C and 15N chemical shift assignments the G4 formed within KRAS22RT sequence.
      PubDate: 2017-11-30
      DOI: 10.1007/s12104-017-9793-0
  • 1 H, 15 N and 13 C backbone resonance assignments of pentaerythritol
           tetranitrate reductase from Enterobacter cloacae PB2
    • Authors: Andreea I. Iorgu; Nicola J. Baxter; Matthew J. Cliff; Jonathan P. Waltho; Sam Hay; Nigel S. Scrutton
      Abstract: Abstract Pentaerythritol tetranitrate reductase (PETNR) is a flavoenzyme possessing a broad substrate specificity and is a member of the Old Yellow Enzyme family of oxidoreductases. As well as having high potential as an industrial biocatalyst, PETNR is an excellent model system for studying hydrogen transfer reactions. Mechanistic studies performed with PETNR using stopped-flow methods have shown that tunneling contributes towards hydride transfer from the NAD(P)H coenzyme to the flavin mononucleotide (FMN) cofactor and fast protein dynamics have been inferred to facilitate this catalytic step. Herein, we report the near-complete 1H, 15N and 13C backbone resonance assignments of PETNR in a stoichiometric complex with the FMN cofactor in its native oxidized form, which were obtained using heteronuclear multidimensional NMR spectroscopy. A total of 97% of all backbone resonances were assigned, with 333 out of a possible 344 residues assigned in the 1H–15N TROSY spectrum. This is the first report of an NMR structural study of a flavoenzyme from the Old Yellow Enzyme family and it lays the foundation for future investigations of functional dynamics in hydride transfer catalytic mechanism.
      PubDate: 2017-11-22
      DOI: 10.1007/s12104-017-9791-2
  • 1 H, 13 C, and 15 N resonance assignments of FAS1-IV domain of human
           periostin, a component of extracellular matrix proteins
    • Authors: Hyosuk Yun; Eun-Hee Kim; Chul Won Lee
      Abstract: Abstract Periostin, an extracellular matrix protein, is secreted by fibroblasts and is overexpressed in various types of cancers. The four internal repeat fasciclin 1 (FAS1) domains of human periostin play crucial roles in promoting tumor metastasis and progression via interaction with cell surface integrins. Among four FAS1 domains of human periostin, the fourth FAS1 domain (FAS1-IV) was prepared for NMR study, since only FAS1-IV was highly soluble, and showed a well-dispersed 2D 1H-15N HSQC spectrum. Here, we report nearly complete backbone and side chain resonance assignments and a secondary structural analysis of the FAS1-IV domain as first steps toward the structure determination of FAS1-IV of human periostin.
      PubDate: 2017-10-31
      DOI: 10.1007/s12104-017-9786-z
  • Chemical shift assignment of a thermophile frataxin
    • Authors: Masooma Rasheed; Robert Yan; Geoff Kelly; Annalisa Pastore
      Abstract: Abstract Frataxin is the protein responsible for the genetically-inherited neurodegenerative disease Friedreich’s ataxia caused by partial silencing of the protein and loss of function. Although the frataxin function is not yet entirely clear, it has been associated to the machine that builds iron–sulfur clusters, essential prosthetic groups involved in several processes and is strongly conserved in organisms from bacteria to humans. Two of its important molecular partners are the protein NFS1 (or IscS in bacteria), that is the desulfurase which converts cysteine to alanine and produces sulfur, and ISU (or IscU), the scaffold protein which transiently accepts the cluster. While bacterial frataxin has been extensively characterized, only few eukaryotic frataxins have been described. Here we report the 1H, 13C and 15N backbone and side-chain chemical shift assignments of frataxin from Chaetomium thermophilum, a thermophile increasingly used by virtue of its stability.
      PubDate: 2017-10-31
      DOI: 10.1007/s12104-017-9790-3
  • NMR assignments of the N-terminal signaling domain of the TonB-dependent
           outer membrane transducer PupB
    • Authors: Jaime L. Jensen; Qiong Wu; Christopher L. Colbert
      Abstract: Abstract Outer membrane TonB-dependent transducers (TBDTs) actively transport ferric siderophore complexes from the extracellular environment into Gram-negative bacteria. They also participate in a cell-surface signaling regulatory pathway that results in upregulation of the transducer itself, in response to iron-deplete conditions. The TBDT PupB transports ferric pseudobactin, and signals through its N-terminal signaling domain (NTSD), while the TBDT homolog PupA is signaling-inactive. Here, we report the NMR chemical shift assignments of the PupB-NTSD. This information will provide the basis for structural characterization of the PupB-NTSD to further explore its signaling properties.
      PubDate: 2017-10-25
      DOI: 10.1007/s12104-017-9785-0
  • 1 H, 13 C and 15 N chemical shift assignment of lissencephaly-1 homology
           (LisH) domain homodimer of human two-hybrid-associated protein 1 with
           RanBPM (Twa1)
    • Authors: Talita S. de Araujo; Marcius S. Almeida
      Abstract: Abstract The CTLH complex is a large, highly conserved eukaryotic complex composed of eight proteins that has been associated to several cellular functions, more often described as an E3 ubiquitin ligase complex involved in protein degradation through ubiquitination but also via vacuole-dependent degradation. A common feature observed in several components of this complex is the presence of the domains lissencephaly-1 homology (LisH) and C-terminal to LisH (CTLH). The LisH domain is found in several proteins involved in chromosome segregation, microtubule dynamics, and cell migration. Also, this domain participates in protein dimerization, besides affecting protein half-life, and influencing in specific cellular localization. Among the proteins found in the CTLH complex, Twa1 (Two-hybrid-associated protein 1 with RanBPM), also known as Gid8 (glucose-induced degradation protein 8 homolog) is the smallest, being a good model for structural studies by NMR. In this work we report the chemical shift assignments of the homodimeric LisH domain of Twa1, as a first step to determine its solution structure.
      PubDate: 2017-10-24
      DOI: 10.1007/s12104-017-9787-y
  • Backbone 1 H, 13 C and 15 N resonance assignments of the OB domain of the
           single stranded DNA-binding protein hSSB2 (NABP1/OBFC2A) and chemical
           shift mapping of the DNA-binding interface
    • Authors: Ruvini Kariawasam; Maddison Knight; Roland Gamsjaeger; Liza Cubeddu
      Abstract: Abstract Single stranded DNA-binding proteins (SSBs) are essential for the maintenance of genome integrity and are required in in all known cellular organisms. Over the last 10 years, the role of two new human SSBs, hSSB1 (NABP2/OBFC2B) and hSSB2 (NABP1/OBFC2A), has been described and characterised in various important DNA repair processes. Both these proteins are made up of a conserved oligonucleotide-binding (OB) fold that is responsible for ssDNA recognition as well a unique flexible carboxy-terminal extension involved in protein–protein interactions. Due to their similar domain organisation, hSSB1 and hSSB2 have been found to display some overlapping functions. However, several studies have also revealed cell- and tissue-specific roles for these two proteins, most likely due to small but significant differences in the protein sequence of the OB domains. While the molecular details of ssDNA binding by hSSB1 has been studied extensively, comparatively little is known about hSSB2. In this study, we use NMR solution-state backbone resonance assignments of the OB domain of hSSB2 to map the ssDNA interaction interface. Our data reveal that ssDNA binding by hSSB2 is driven by four key aromatic residues in analogy to hSSB1, however, some significant differences in the chemical shift perturbations are observed, reflecting differences in ssDNA recognition. Future studies will aim at determining the structural basis of these differences and thus help to gain a more comprehensive understanding of the functional divergences that these novel hSSBs display in the context of genome maintenance.
      PubDate: 2017-10-24
      DOI: 10.1007/s12104-017-9789-9
  • 1 H, 15 N, 13 C backbone resonance assignment of the C-terminal domain of
           enzyme I from Thermoanaerobacter tengcongensis
    • Authors: Rochelle Rea Dotas; Vincenzo Venditti
      Abstract: Abstract Phosphoenolpyruvate binding to the C-terminal domain (EIC) of enzyme I of the bacterial phosphotransferase system (PTS) initiates a phosphorylation cascade that results in sugar translocation across the cell membrane and controls a large number of essential pathways in bacterial metabolism. EIC undergoes an expanded to compact conformational equilibrium that is regulated by ligand binding and determines the phosphorylation state of the overall PTS. Here, we report the backbone 1H, 15N and 13C chemical shift assignments of the 70 kDa EIC dimer from the thermophilic bacterium Thermoanaerobacter tengcongensis. Assignments were obtained at 70 °C by heteronuclear multidimensional NMR spectroscopy. In total, 90% of all backbone resonances were assigned, with 264 out of a possible 299 residues assigned in the 1H–15N TROSY spectrum. The secondary structure predicted from the assigned backbone resonance using the program TALOS+ is in good agreement with the X-ray crystal structure of T. tengcongensis EIC. The reported assignments will allow detailed structural and thermodynamic investigations on the coupling between ligand binding and conformational dynamics in EIC.
      PubDate: 2017-10-24
      DOI: 10.1007/s12104-017-9788-x
  • 1 H, 13 C and 15 N backbone resonance assignments of the β-lactamase BlaP
           from Bacillus licheniformis 749 / C and two mutational variants
    • Authors: David Thorn; Jennifer Kay; Noureddine Rhazi; Mireille Dumoulin; Alessandra Corazza; Christian Damblon
      Abstract: Abstract Class A β-lactamases have been widely used as versatile scaffolds to create hybrid (or chimeric) proteins for a series of applications ranging from basic research to medicine. We have, in particular, used the β-lactamase BlaP from Bacillus licheniformis 749/C (BlaP) as a protein scaffold to create model polyglutamine (polyQ) proteins in order to better understand the mechanism(s) by which an expanded polyQ sequence triggers the formation of amyloid fibrils. The model chimeras were designed by inserting a polyQ sequence of various lengths at two different locations within BlaP (i.e. position 197 or position 216) allowing a detailed comparison of the effects of subtle differences in the environment of the polyQ sequence on its ability to trigger protein aggregation. In order to investigate the effects of the polyQ insertion at both positions on the structure, stability and dynamics of BlaP, a series of NMR experiments including H/D exchange are foreseen. Accordingly, as necessitated by these studies, here we report the NMR assignment of the wild-type BlaP (BlaP-WT) and of the two reference proteins, BlaP197Q0 and BlaP216Q0, wherein a Pro-Gly dipeptide has been introduced at position 197 and 216, respectively; this dipeptide originates from the addition of the Sma1 restriction site at the genetic level to allow further polyQ sequence insertion.
      PubDate: 2017-10-13
      DOI: 10.1007/s12104-017-9782-3
  • NMR assignments of the N-terminal domain of Staphylococcus aureus
           hibernation promoting factor (SaHPF)
    • Authors: Konstantin S. Usachev; Rustam Kh. Ayupov; Shamil Z. Validov; Iskander Sh. Khusainov; Marat M. Yusupov
      Abstract: Abstract Staphylococcus aureus: hibernation-promoting factor (SaHPF) is a 22.2 kDa stationary-phase protein that binds to the ribosome and turns it to the inactive form favoring survival under stress. Sequence analysis has shown that this protein is combination of two homolog proteins obtained in Escherichia coli—ribosome hibernation promoting factor (HPF) (11,000 Da) and ribosome modulation factor RMF (6500 Da). Binding site of E. coli HPF on the ribosome have been shown by X-ray study of Thermus thermophilus ribosome complex. Hence, recent studies reported that the interface is markedly different between 100S from S. aureus and E. coli. Cryo-electron microscopy structure of 100S S. aureus ribosomes reveal that the SaHPF-NTD binds to the 30S subunit as observed for shorter variants of HPF in other species and the C-terminal domain (CTD) protrudes out of each ribosome in order to mediate dimerization. SaHPF-NTD binds to the small subunit similarly to its homologs EcHPF, EcYfiA, and a plastid-specific YfiA. Furthermore, upon binding to the small subunit, the SaHPF-NTD occludes several antibiotic binding sites at the A site (hygromycin B, tetracycline), P site (edeine) and E site (pactamycin, kasugamycin). In order to elucidate the structure, dynamics and function of SaHPF-NTD from S. aureus, here we report the backbone and side chain resonance assignments for SaHPF-NTD. Analysis of the backbone chemical shifts by TALOS+ suggests that SaHPF-NTD contains two α-helices and four β-strands (β1-α1-β2-β3-β4-α2 topology). Investigating the long-term survival of S. aureus and other bacteria under antibiotic pressure could lead to advances in antibiotherapy.
      PubDate: 2017-10-04
      DOI: 10.1007/s12104-017-9783-2
  • Backbone resonance assignments of complexes of human voltage-dependent
           sodium channel Na V 1.2 IQ motif peptide bound to apo calmodulin and to
           the C-domain fragment of apo calmodulin
    • Authors: Ryan Mahling; Adina M. Kilpatrick; Madeline A. Shea
      Abstract: Abstract Human voltage-gated sodium channel NaV1.2 has a single pore-forming α-subunit and two transmembrane β-subunits. Expressed primarily in the brain, NaV1.2 is critical for initiation and propagation of action potentials. Milliseconds after the pore opens, sodium influx is terminated by inactivation processes mediated by regulatory proteins including calmodulin (CaM). Both calcium-free (apo) CaM and calcium-saturated CaM bind tightly to an IQ motif in the C-terminal tail of the α-subunit. Our thermodynamic studies and solution structure (2KXW) of a C-domain fragment of apo 13C,15N- CaM (CaMC) bound to an unlabeled peptide with the sequence of rat NaV1.2 IQ motif showed that apo CaMC (a) was necessary and sufficient for binding, and (b) bound more favorably than calcium-saturated CaMC. However, we could not monitor the NaV1.2 residues directly, and no structure of full-length CaM (including the N-domain of CaM (CaMN)) was determined. To distinguish contributions of CaMN and CaMC, we used solution NMR spectroscopy to assign the backbone resonances of a complex containing a 13C,15N-labeled peptide with the sequence of human NaV1.2 IQ motif (NaV1.2IQp) bound to apo 13C,15N-CaM or apo 13C,15N-CaMC. Comparing the assignments of apo CaM in complex with NaV1.2IQp to those of free apo CaM showed that residues within CaMC were significantly perturbed, while residues within CaMN were essentially unchanged. The chemical shifts of residues in NaV1.2IQp and in the C-domain of CaM were nearly identical regardless of whether CaMN was covalently linked to CaMC. This suggests that CaMN does not influence apo CaM binding to NaV1.2IQp.
      PubDate: 2017-08-19
      DOI: 10.1007/s12104-017-9767-2
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