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https://www.readbyqxmd.com/read/28918554/genome-wide-identification-classification-evolutionary-analysis-and-gene-expression-patterns-of-the-protein-kinase-gene-family-in-wheat-and-aegilops-tauschii
#1
Jun Yan, Peisen Su, Zhaoran Wei, Eviatar Nevo, Lingrang Kong
In this study we systematically identified and classified PKs in Triticum aestivum, Triticum urartu and Aegilops tauschii. Domain distribution and exon-intron structure analyses of PKs were performed, and we found conserved exon-intron structures within the exon phases in the kinase domain. Collinearity events were determined, and we identified various T. aestivum PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed that some PKs might participate in the signaling pathways of stress response and developmental processes...
September 16, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28918549/loss-of-lhci-system-affects-lhcii-re-distribution-between-thylakoid-domains-upon-state-transitions
#2
Mauro Bressan, Roberto Bassi, Luca Dall'Osto
LHCI, the peripheral antenna system of Photosystem I, includes four light-harvesting proteins (Lhca1-Lhca4) in higher plants, all of which are devoid in the Arabidopsis thaliana knock-out mutant ΔLhca. PSI absorption cross-section was reduced in the mutant, thus affecting the redox balance of the photosynthetic electron chain and resulting in a more reduced PQ with respect to the wild type. ΔLhca plants developed compensatory response by enhancing LHCII binding to PSI. However, the amplitude of state transitions, as measured from changes of chlorophyll fluorescence in vivo, was unexpectedly low than the high level of PSI-LHCII supercomplex established...
September 16, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28918320/in-silico-interaction-analysis-of-cannabinoid-receptor-interacting-protein-1b-crip1b-cb1-cannabinoid-receptor
#3
Pratishtha Singh, Anjali Ganjiwale, Allyn C Howlett, Sudha M Cowsik
Cannabinoid Receptor Interacting Protein isoform 1b (CRIP1b) is known to interact with the CB1 receptor. Alternative splicing of the CNRIP1 gene produces CRIP1a and CRIP1b with a difference in the third exon only. Exons 1 and 2 encode for a functional domain in both proteins. CRIP1a is involved in regulating CB1 receptor internalization, but the function of CRIP1b is not very well characterized. Since there are significant identities in functional domains of these proteins, CRIP1b is a potential target for drug discovery...
September 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28917892/a-mechanism-for-the-synergistic-gelation-properties-of-gelatin-b-and-xanthan-gum-aqueous-mixtures
#4
Chang-Sheng Wang, Nick Virgilio, Paula Wood-Adams, Marie-Claude Heuzey
Gelatin B and xanthan gum aqueous mixtures (GB/XG, (0.2-2%)/0.2% w/v) exhibit enhanced gelling properties compared to their pure component solutions at similar compositions. The mixed gels comprise co-localized networks of GB and XG-rich domains. Our results show that these domains are composed of intermolecular complexes and their aggregates stabilized by the neutralization effect of GB, and linked together by formation of GB triple helices. GB/XG mixtures display composition-dependent microstructural transitions: from discontinuous aggregates (GB/XG ratio≤1) to a continuous GB/XG network (ratio=2-6), followed by network fragmentation (ratio=8-10)...
November 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28917843/rapgef2-a-guanine-nucleotide-exchange-factor-for-rap1-small-gtpases-plays-a-crucial-role-in-adherence-junction-aj-formation-in-radial-glial-cells-through-erk-mediated-upregulation-of-the-aj-constituent-protein-expression
#5
Maged Ibrahim Farag, Yoko Yoshikawa, Kazuhiro Maeta, Tohru Kataoka
Rapgef2 and Rapgef6 define a subfamily of guanine nucleotide exchange factors for Rap1, characterized by possession of the Ras/Rap-associating domains and implicated in the etiology of schizophrenia. We previously found that dorsal telencephalon-specific Rapgef2 conditional knockout mice exhibits severe defects in formation of apical surface adherence junctions (AJs) and localization of radial glial cells (RGCs). In this study, we analyze the underlying molecular mechanism by using primary cultures of RGCs established from the developing cerebral cortex...
September 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28917841/graphene-vp40-interactions-and-potential-disruption-of-the-ebola-virus-matrix-filaments
#6
Jeevan B Gc, Rudramani Pokhrel, Nisha Bhattarai, Kristen A Johnson, Bernard S Gerstman, Robert V Stahelin, Prem P Chapagain
Ebola virus infections cause hemorrhagic fever that often results in very high fatality rates. In addition to exploring vaccines, development of drugs is also essential for treating the disease and preventing the spread of the infection. The Ebola virus matrix protein VP40 exists in various conformational and oligomeric forms and is a potential pharmacological target for disrupting the virus life-cycle. Here we explored graphene-VP40 interactions using molecular dynamics simulations and graphene pelleting assays...
September 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28917589/a-novel-rgl2-dof6-complex-contributes-to-primary-seed-dormancy-in-arabidopsis-thaliana-by-regulating-a-gata-transcription-factor
#7
Pratibha Ravindran, Vivek Verma, Petra Stamm, Prakash P Kumar
The DELLA protein RGA-LIKE2 (RGL2) is a key transcriptional repressor of gibberellic acid (GA) signaling that regulates seed germination. We identified GATA12, a gene encoding a GATA-type zinc finger transcription factor, as one of the downstream targets of RGL2 in Arabidopsis thaliana. Our data show that freshly harvested (unstratified) seeds of GATA12 antisense suppression lines have reduced dormancy than the wild type, while ectopic expression lines show enhanced seed dormancy. We show that GATA12 transcription is negatively regulated by GA and its transcript levels decline dramatically under dormancy-breaking conditions such as dry storage and cold-stratification of seeds...
September 13, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28917202/mechanisms-of-maguk-mediated-cellular-junctional-complex-organization
#8
REVIEW
Fei Ye, Menglong Zeng, Mingjie Zhang
Membrane-associated guanylate kinases (MAGUKs) are a family of scaffold proteins that are enriched in cellular junctions and essential for tissue development and homeostasis. Mutations of MAGUKs are linked to many human diseases including cancers, psychiatric disorders, and intellectual disabilities. MAGUKs share a common PDZ-SH3-GK tandem domain organization at the C-terminal end. In this review, we summarize the mechanistic basis governing target recognition and regulations of this binding by the PDZ-SH3-GK tandem of various MAGUKs...
September 13, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28916791/genomic-structure-and-evolution-of-the-mating-type-locus-in-the-green-seaweed-ulva-partita
#9
Tomokazu Yamazaki, Kensuke Ichihara, Ryogo Suzuki, Kenshiro Oshima, Shinichi Miyamura, Kazuyoshi Kuwano, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Masahira Hattori, Shigeyuki Kawano
The evolution of sex chromosomes and mating loci in organisms with UV systems of sex/mating type determination in haploid phases via genes on UV chromosomes is not well understood. We report the structure of the mating type (MT) locus and its evolutionary history in the green seaweed Ulva partita, which is a multicellular organism with an isomorphic haploid-diploid life cycle and mating type determination in the haploid phase. Comprehensive comparison of a total of 12.0 and 16.6 Gb of genomic next-generation sequencing data for mt(-) and mt(+) strains identified highly rearranged MT loci of 1...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916774/the-mechano-sensing-role-of-the-unique-sh3-insertion-in-plakin-domains-revealed-by-molecular-dynamics-simulations
#10
Csaba Daday, Katra Kolšek, Frauke Gräter
The plakin family of proteins, important actors in cross-linking force-bearing structures in the cell, contain a curious SH3 domain insertion in their chain of spectrin repeats (SRs). While SH3 domains are known to mediate protein-protein interactions, here, its canonical binding site is autoinhibited by the preceding SR. Under force, however, this SH3 domain could be released, and possibly launch a signaling cascade. We performed large-scale force-probe molecular dynamics simulations, across two orders of magnitude of loading rates, to test this hypothesis, on two prominent members of the plakin family: desmoplakin and plectin, obligate proteins at desmosomes and hemidesmosomes, respectively...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916764/rapid-and-reversible-epigenome-editing-by-endogenous-chromatin-regulators
#11
Simon M G Braun, Jacob G Kirkland, Emma J Chory, Dylan Husmann, Joseph P Calarco, Gerald R Crabtree
Understanding the causal link between epigenetic marks and gene regulation remains a central question in chromatin biology. To edit the epigenome we developed the FIRE-Cas9 system for rapid and reversible recruitment of endogenous chromatin regulators to specific genomic loci. We enhanced the dCas9-MS2 anchor for genome targeting with Fkbp/Frb dimerizing fusion proteins to allow chemical-induced proximity of a desired chromatin regulator. We find that mSWI/SNF (BAF) complex recruitment is sufficient to oppose Polycomb within minutes, leading to activation of bivalent gene transcription in mouse embryonic stem cells...
September 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28916724/a-novel-mechanism-for-ca-2-calmodulin-dependent-protein-kinase-ii-targeting-to-l-type-ca-2-channels-that-initiates-long-range-signaling-to-the-nucleus
#12
Xiaohan Wang, Christian R Marks, Tyler L Perfitt, Terunaga Nakagawa, Amy Lee, David A Jacobson, Roger J Colbran
Neuronal excitation can induce new mRNA transcription, a phenomenon called excitation-transcription (E-T) coupling. Among several pathways implicated in E-T coupling, activation of voltage-gated L-type Ca(2+) channels (LTCCs) in the plasma membrane can initiate a signaling pathway that ultimately increases nuclear CREB phosphorylation and, in most cases, expression of immediate early genes. Initiation of this long-range pathway has been shown to require recruitment of Ca(2+)-sensitive enzymes to a nanodomain in the immediate vicinity of the LTCC by an unknown mechanism...
September 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28916707/pqn-75-is-expressed-in-the-pharyngeal-gland-cells-of-caenorhabditiselegans-and-is-dispensable-for-germline-development
#13
Jesse D Rochester, Paige C Tanner, Catherine S Sharp, Karolina M Andralojc, Dustin L Updike
In Caenorhabditis elegans, five pharyngeal gland cells reside in the terminal bulb of the pharynx and extend anterior processes to five contact points in the pharyngeal lumen. Pharyngeal gland cells secrete mucin-like proteins thought to facilitate digestion, hatching, molting and assembly of the surface coat of the cuticle, but supporting evidence has been sparse. Here we show pharyngeal gland cell expression of PQN-75, a unique protein containing an N-terminal signal peptide, nucleoporin (Nup)-like phenylalanine/glycine (FG) repeats, and an extensive polyproline repeat domain with similarities to human basic salivary proline-rich pre-protein PRB2...
September 15, 2017: Biology Open
https://www.readbyqxmd.com/read/28916410/kinetic-stability-and-sequence-structure-studies-of-urine-derived-bence-jones-proteins-from-multiple-myeloma-and-light-chain-amyloidosis-patients
#14
Luis M Blancas-Mejía, Emily B Martin, Angela Williams, Jonathan S Wall, Marina Ramirez-Alvarado
It is now accepted that the ability of a protein to form amyloid fibrils could be associated both kinetic and thermodynamic protein folding parameters. A recent study from our laboratory using recombinant full-length (encompassing the variable and constant domain) immunoglobulin light chains found a strong kinetic control of the protein unfolding for these proteins. In this study, we are extending our analysis by using urine-derived Bence Jones proteins (BJPs) from five patients with light chain (AL) amyloidosis and four patients with multiple myeloma (MM)...
September 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28916391/zika-virus-structural-biology-and-progress-in-vaccine-development
#15
REVIEW
Hsiao-Han Lin, Bak-Sau Yip, Li-Min Huang, Suh-Chin Wu
The growing number of zika virus (ZIKV) infections plus a 20-fold increase in neonatal microcephaly in newborns in Brazil have raised alarms in many countries regarding the threat to pregnant women. Instances of microcephaly and central nervous system malformations continue to increase in ZIKV outbreak regions. ZIKV is a small enveloped positive-strand RNA virus belonging to the Flavivirus genus of the Flaviviridae family. High-resolution ZIKV structures recently identified by cryo-electron microscopy indicate that the overall ZIKV structure is similar to those of other flaviviruses...
September 12, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28916386/molecular-mechanisms-of-the-r61t-mutation-in-apolipoprotein-e4-a-dynamic-rescue
#16
Benfeard Williams, Marino Convertino, Jhuma Das, Nikolay V Dokholyan
The apolipoprotein E4 (ApoE4) gene is the strongest genetic risk factor for Alzheimer's disease (AD). With respect to the other common isoforms of this protein (ApoE2 and ApoE3), ApoE4 is characterized by lower stability that underlies the formation of a stable interaction between the protein's N- and C-terminal domains. AD-related cellular dysfunctions have been linked to this ApoE4 misfolded state. In this regard, it has been reported that the mutation R61T is able to rescue the deleterious cellular effects of ApoE4 by preventing the formation of the misfolded intermediate state...
September 12, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28916383/heterologous-expression-and-structure-function-relationship-of-low-temperature-and-alkaline-active-protease-from-acinetobacter-sp-ihb-b-5011-mn12
#17
Richa Salwan, Vivek Sharma, Mohinder Pal, Ramesh Chand Kasana, Sudesh Kumar Yadav, Arvind Gulati
The gene encoding protease from Acinetobacter sp. IHB B 5011(MN12) was cloned and expressed in Escherichia coli BL21(DE3). The nucleotide sequence revealed 1323bp ORF encoding 441 amino acids protein with molecular weight 47.2kDa. The phylogenetic analysis showed clustering of Alp protease with subtilisin-like serine proteases of S8 family. The amino acid sequence was comprised of N-terminal signal peptide 1-21 amino acids, pre-peptide 22-143 amino acids, peptidase S8 domain 144-434 amino acids, and pro-peptide 435-441 amino acids at C-terminus...
September 12, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28916380/roles-of-amino-acid-residues-h66-and-d326-in-the-creatine-kinase-activity-and-structural-stability
#18
Qing-Yun Wu, Fang Wei, Yuan-Yuan Zhu, Yu-Xue Tong, Jiang Cao, Ping Zhou, Zhen-Yu Li, Ling-Yu Zeng, Feng Li, Xiao-Yun Wang, Kai-Lin Xu
Creatine kinase (CK) is a key enzyme for cellular energy metabolism, catalyzing the reversible phosphoryl transfer from phosphocreatine to ADP in vertebrates. CK contains a pair of highly conserved amino acids (H66 and D326) which might play an important role in sustaining the compact structure of CK by linking its N- and C- terminal domains; however the mechanism is still unclear. In this study, spectroscopic, structural modeling and protein folding experiments suggested that D326A, H66P and H66P/D326A mutations led to disruption of the hydrogen bond between those two amino acid residues and form the partially unfolded state which made it easier to be inactivated and unfolded under environmental stresses, and more prone to form insoluble aggregates...
September 12, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28916359/a-class-b-scavenger-receptor-from-eriocheir-sinensis-essr-b1-restricts-bacteria-proliferation-by-promoting-phagocytosis
#19
Yao-Meng Wu, Lei Yang, Xue-Jie Li, Lu Li, Qun Wang, Wei-Wei Li
Scavenger receptors (SRs) are important pattern recognition receptors (PRRs), which play significant roles in host defense against pathogens by identifying pathogen-associated molecular patterns (PAMPs). In this study, we report the cloning and characterization of a SR from Eriocheir sinensis (EsSR-B1) which is a 500 amino acid protein encoded by a gene comprised of 2726 nucleotides with a 1503 bp open reading frame. The domains of EsSR-B1 were found to be evolutionarily conserved. EsSR-B1 was widely detected in different tissues of E...
September 12, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28916358/the-functional-characterization-and-comparison-of-two-single-crd-containing-c-type-lectins-with-novel-and-typical-key-motifs-from-portunus-trituberculatus
#20
Mengmeng Huang, Changkao Mu, Yuehong Wu, Fei Ye, Dan Wang, Cong Sun, Zhengbing Lv, Bingnan Han, Chunlin Wang, Xue-Wei Xu
C-type lectins are a superfamily of Ca(2+)-dependent carbohydrate-recognition proteins, which play crucial roles in innate immunity including nonself-recognition and pathogen elimination. In the present study, two single-CRD containing C-type lectins were identified from swimming crab Portunus trituberculatus (designated as PtCTL-2 and PtCTL-3). The open reading frame (ORF) of PtCTL-2 encoded polypeptides of 485 amino acids with a signal peptide and a single carbohydrate-recognition domain (CRD), while PtCTL-3's ORF encoded polypeptides of 241 amino acids with a coiled-coil region and a single-CRD...
September 12, 2017: Fish & Shellfish Immunology
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