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https://www.readbyqxmd.com/read/29236385/lipoxygenases-and-their-metabolites-in-formation-of-plant-stress-tolerance
#1
L M Babenko, M M Shcherbatiuk, T D Skaterna, I V Kosakivska
The review focuses on the analysis of new information concerning molecular enzymology of lipoxygenases – proteins involved in lipid peroxidation and found in animals and plants. Modern concept of structural features, catalytic characteristics and functions of lipoxygenase family enzymes as well as products of their catalytic activity in plants have been discussed and summarized. Issues of enzyme localization in plant cells and tissues, evolution and distribution of lipoxygenases, involvement in production of signaling substances involved in formation of adaptation response to abiotic and biotic stress factors and in regulation of lipoxygenase signal system activity are highlighted...
January 2017: Ukrainian Biochemical Journal
https://www.readbyqxmd.com/read/29236365/species-differences-in-the-organization-of-the-ventral-cochlear-nucleus
#2
Joan S Baizer, Keit Men Wong, Richard J Salvi, Senthilvelan Manohar, Chet C Sherwood, Patrick R Hof, James F Baker, Sandra F Witelson
The mammalian cochlear nuclei (CN) consist of two major subdivisions, the dorsal (DCN) and ventral (VCN) nuclei. We previously reported differences in the structural and neurochemical organization of the human DCN from that in several other species. Here we extend this analysis to the VCN, considering both the organization of subdivisions and the types and distributions of neurons. Classically, the VCN in mammals is composed of two subdivisions, the anteroventral (VCA) and posteroventral cochlear nuclei (VCP)...
December 13, 2017: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/29236299/apicomplexa-specific-%C3%AE-hairpin-of-plasmodium-and-toxoplasma-profilins-a-molecular-dynamics-simulation-study
#3
Priyadarsini Kadirvel, Sharmila Anishetty
Profilin is one of the actin-binding proteins that regulate dynamics of actin polymerization. It plays a key role in cell motility and invasion. It also interacts with several other proteins notably through its poly-L-proline (PLP) binding site. Profilin in apicomplexa is characterized by a unique mini-domain consisting of a large β-hairpin extension and an acidic loop which is relatively longer in Plasmodium species. Profilin is essential for the invasive blood stages of Plasmodium falciparum. In the current study, unbound profilins from Plasmodium falciparum (Pf), Toxoplasma gondii (Tg) and Homo sapiens (Hs) were subjected to molecular dynamics (MD) simulations for a timeframe of 100 ns each to understand the conformational dynamics of these proteins...
December 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29236298/leptin-a-new-therapeutic-target-for-treatment-of-diabetes-mellitus
#4
Kanwal Rehman, Muhammad Sajid Hamid Akash, Zunaira Alina
Leptin is an endogenous protein having 167 amino acids and is derived from adipocytes. It hass tertiary structure that resembles with that of the pro-inflammatory cytokines family. The fundamental role of leptin is to maintain the energy homeostasis with the aid of its counter hormone called ghrelin, known as the "hunger hormone". Small quantities of leptin are also present in various tissues like ovary, placenta, pituitary gland, mammary gland, skeletal muscle, stomach and lymphoid tissue. Expression of leptin is strongly associated with various inflammatory responses and immune system, and plays crucial role in the pathophysiology of obesity and development of diabetes mellitus (DM) and insulin resistance...
December 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29236213/structural-probing-screening-and-structure-based-drug-repositioning-insights-into-the-identification-of-potential-cox-2-inhibitors-from-selective-coxibs
#5
Uma Devi Bommu, Kranthi Kumar Konidala, Rishika Pamanji, Suneetha Yeguvapalli
The rate-limiting enzyme cyclooxygenase-2 (COX-2) is considered as an insightful prognostic target for non-small cell lung cancer (NSCLC) therapy. Now, administration and prolonged utilization of selective COX-2 inhibitors (COXIBs) towards moderating the NSCLC has been associated with different side effects. In the present study, we focused on the structure-based drug repositioning approaches for predicting therapeutic potential de novo candidates for human COX-2. Due to discrepancies in the eminence of x-ray diffraction structures, creates a big barrier in drug discovery approach...
December 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29236185/genome-wide-identification-and-cadmium-induced-expression-profiling-of-sulfate-transporter-sultr-genes-in-sorghum-sorghum-bicolor-l
#6
M Aydın Akbudak, Ertugrul Filiz, Kubra Kontbay
Sulfur is an essential element for all living organisms. Plants can convert inorganic sulfur into organic sulfur compounds by complex enzymatic steps. In this study, we conducted a genome-wide analysis of sulfate transporter genes (SULTRs) in the sorghum (Sorghum bicolor) genome and examined expression profiles of SbSULTR genes under 200 µM cadmium (Cd) exposure. As a result of sorghum genome analysis, 11 SULTR genes were identified, including SbSULTR1;1, SbSULTR1;2, SbSULTR1;3, SbSULTR2;1, SbSULTR2;2, SbSULTR3;1, SbSULTR3;2, SbSULTR3;3, SbSULTR3;4, SbSULTR3;5, and SbSULTR4...
December 13, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/29236145/-non-coding-rna-innovative-regulators-with-therapeutic-perspective
#7
A Bührke, C Bär, T Thum
As a result of the Human Genome Project it became evident that only 1-3% of all gene transcripts encode proteins. The vast majority of gene transcripts are in fact characterized as non-coding RNAs (ncRNAs). These ncRNAs have a huge impact on diverse physiological and pathological mechanisms within an organism. In particular, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), which are differentiated by their size and function, are involved in the regulation and development of many illnesses. In the context of heart and cardiovascular diseases numerous ncRNAs have also already been described in some detail...
December 13, 2017: Herz
https://www.readbyqxmd.com/read/29236079/unexpected-binding-mode-of-a-potent-indeno-1-2-b-indole-type-inhibitor-of-protein-kinase-ck2-revealed-by-complex-structures-with-the-catalytic-subunit-ck2%C3%AE-and-its-paralog-ck2%C3%AE
#8
Jennifer Hochscherf, Dirk Lindenblatt, Benedict Witulski, Robin Birus, Dagmar Aichele, Christelle Marminon, Zouhair Bouaziz, Marc Le Borgne, Joachim Jose, Karsten Niefind
Protein kinase CK2, a member of the eukaryotic protein kinase superfamily, is associated with cancer and other human pathologies and thus an attractive drug target. The indeno[1,2-b]indole scaffold is a novel lead structure to develop ATP-competitive CK2 inhibitors. Some indeno[1,2-b]indole-based CK2 inhibitors additionally obstruct ABCG2, an ABC half transporter overexpressed in breast cancer and co-responsible for drug efflux and resistance. Comprehensive derivatization studies revealed substitutions of the indeno[1,2-b]indole framework that boost either the CK2 or the ABCG2 selectivity or even support the dual inhibition potential...
December 13, 2017: Pharmaceuticals
https://www.readbyqxmd.com/read/29236068/in-silico-screening-and-in-vitro-activity-measurement-of-javamide-analogues-as-potential-p38-mapk-inhibitors
#9
Jae B Park
p38 Mitogen-activated protein kinase (p38 MAPK) is a protein kinase critically involved in the progress of inflammation/stress-associated diseases. Our data suggested that javamide analogues may contain strong anti-inflammation activities, but there is little information about their effects on p38 MAPK. Therefore, in this paper, the effects of thirty javamide analogues on p38 MAPK were investigated using in silico screening and in vitro p38 MAPK assay methods. The javamide analogues were synthesized and their chemical structures were confirmed using nuclear magnetic resonance (NMR) spectroscopic methods...
December 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29235980/restoration-of-glycoprotein-erns-dimerization-via-pseudoreversion-partially-restores-virulence-of-classical-swine-fever-virus
#10
Anna Katharina Tucakov, Sabine Yavuz, Eva-Maria Schürmann, Manjula Mischler, Anne Klingebeil, Gregor Meyers
The classical swine fever virus (CSFV) represents one of the most important pathogens of swine. The CSFV glycoprotein Erns is an essential structural protein and an important virulence factor. The latter is dependent on the RNase activity of this envelope protein and, most likely, its secretion from the infected cell. A further important feature with regard to its function as a virulence factor is the formation of disulfide-linked Erns homodimers that are found in virus-infected cells and virions. Mutant CSFV lacking cysteine (Cys) 171, the residue responsible for intermolecular disulfide bond formation, were found to be attenuated in pigs (Tews BA, Schürmann EM, Meyers G...
December 13, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/29235861/kras-switch-mutants-d33e-and-a59g-crystallize-in-the-state-1-conformation
#11
Jia Lu, Asim Bera, Sudershan R Gondi, Kenneth Dale Westover
KRAS switch loop movements play a crucial role in regulating RAS signaling and alteration in these sensitive dynamics are a principal mechanism through which disease-associated RAS mutations lead to aberrant RAS activation. Prior studies suggest that despite high sequence similarity, the switches in KRAS are more dynamic than HRAS. We solved x-ray crystal structures of the rare tumorigenic KRAS mutants KRASD33E, in switch 1 (SW1), and KRASA59G, in switch 2 (SW2), bound to GDP and found these adopt nearly identical, open SW1 conformations as well as altered SW2 conformations...
December 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/29235855/zinc-ligand-swapping-mediated-complex-formation-and-sulfur-transfer-between-sufs-and-sufu-for-iron-sulfur-cluster-biogenesis-in-bacillus-subtilis
#12
Takashi Fujishiro, Takuya Terahata, Kouhei Kunichika, Nao Yokoyama, Chihiro Maruyama, Kei Asai, Yasuhiro Takahashi
SufU is a zinc-containing protein involved in mobilization of sulfur from SufS for iron-sulfur cluster biogenesis of Bacillus subtilis. Structural basis for the sulfur transfer in SufS-SufU complex was revealed. A zinc-ligand exchange reaction upon SufS-SufU complexation provides a free thiol from Cys41 of SufU as a sulfur acceptor.
December 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29235845/structure-based-identification-of-hiv-1-nucleocapsid-protein-inhibitors-active-against-wild-type-and-drug-resistant-hiv-1-strains
#13
Mattia Mori, Lesia Kovalenko, Savina Malancona, Francesco Saladini, Davide De Forni, Manuel Pires, Nicolas Humbert, Eleonore Real, Thomas Botzanowski, Sarah Cianférani, Alessia Giannini, Maria Chiara Dasso Lang, Giulia Cugia, Barbara Poddesu, Franco Lori, Maurizio Zazzi, Steven Harper, Vincenzo Summa, Yves Mély, Maurizio Botta
HIV/AIDS is still one of the leading causes of death worldwide. Current drugs that target the canonical steps of HIV-1 life cycle are efficient in blocking viral replication, but are unable to eradicate HIV-1 from infected patients. Moreover, drug resistance (DR) is often associated with the clinical use of these molecules, thus raising the need for novel drug candidates as well as novel putative drug targets. In this respect, pharmacological inhibition of the highly conserved and multifunctional nucleocapsid protein (NC) of HIV-1 is considered a promising alternative to current drugs, particularly to overcome DR...
December 13, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29235590/unravelling-the-hydrophobicity-of-urea-in-water-using-thermodiffusion-implications-for-protein-denaturation
#14
Doreen Niether, Silvia Di Lecce, Fernando Bresme, Simone Wiegand
Urea is widely used as a protein denaturant in aqueous solutions. Experimental and computer simulation studies have shown that it dissolves in water almost ideally at high concentrations, introducing little disruption in the water hydrogen bonded structure. However, at concentrations of the order of 5 M or higher, urea induces denaturation in a wide range of proteins. The origin of this behaviour is not completely understood, but it is believed to stem from a balance between urea-protein and urea-water interactions, with urea becoming possibly hydrophobic at a specific concentration range...
December 13, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29235505/comprehensive-analysis-of-the-catalytic-and-structural-properties-of-a-mu-class-glutathione-s-transferase-from-fasciola-gigantica
#15
Jupitara Kalita, Rohit Shukla, Harish Shukla, Kundlik Gadhave, Rajanish Giri, Timir Tripathi
Glutathione S‒transferases (GSTs) play an important role in the detoxification of xenobiotics. They catalyze the nucleophilic addition of glutathione (GSH) to nonpolar compounds, rendering the products water-soluble. In the present study, we investigated the catalytic and structural properties of a mu-class GST from Fasciola gigantica (FgGST1). The purified recombinant FgGST1 formed a homodimer composed of 25 kDa subunit. Kinetic analysis revealed that FgGST1 displays broad substrate specificity and shows high GSH conjugation activity toward 1-chloro-2,4-dinitrobenzene, 4-nitroquinoline-1-oxide, and trans-4-phenyl-3-butene-2-one and peroxidase activity towards trans-2-nonenal and hexa-2,4-dienal...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235494/molecular-cloning-and-expression-analysis-of-two-key-genes-hds-and-hdr-in-the-mep-pathway-in-pyropia-haitanensis
#16
Yuan He, Zhihong Yan, Yu Du, Yafeng Ma, Songdong Shen
The 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate synthase (HDS) gene and the 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase (HDR) gene are two important genes in the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. In this study, we reported the isolation and characterization of full-length HDS (MF101802) and HDR (MF159558) from Pyropia haitanensis. Characteristics of 3-D structures of the PhHDS and PhHDR proteins were analysed respectively. The results showed that the full-length cDNA of PhHDS, which is 1801 bp long, contained a 1455 bp open reading frame (ORF) encoding a putative 484 amino acid residue protein with a predicted molecular mass of 51...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235477/nucleotide-and-mal3-dependent-changes-in-fission-yeast-microtubules-suggest-a-structural-plasticity-view-of-dynamics
#17
Ottilie von Loeffelholz, Neil A Venables, Douglas Robert Drummond, Miho Katsuki, Robert Cross, Carolyn A Moores
Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo-electron tomography reveals that microtubules assembled from S. pombe tubulin have predominantly B-lattice interprotofilament contacts, with protofilaments skewed around the microtubule axis. Copolymerization with Mal3 favors 13 protofilament microtubules with reduced protofilament skew, indicating that Mal3 adjusts interprotofilament interfaces...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29235471/ctcf-driven-terra-transcription-facilitates-completion-of-telomere-dna-replication
#18
Kate Beishline, Olga Vladimirova, Stephen Tutton, Zhuo Wang, Zhong Deng, Paul M Lieberman
Telomere repeat DNA forms a nucleo-protein structure that can obstruct chromosomal DNA replication, especially under conditions of replication stress. Transcription of telomere repeats can initiate at subtelomeric CTCF-binding sites to generate telomere repeat-encoding RNA (TERRA), but the role of transcription, CTCF, and TERRA in telomere replication is not known. Here, we have used CRISPR/Cas9 gene editing to mutate CTCF-binding sites at the putative start site of TERRA transcripts for a class of subtelomeres...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29235445/direct-three-dimensional-printing-of-polymeric-scaffolds-with-nanofibrous-topography
#19
Aruna Prasopthum, Kevin Shakesheff, Jing Yang
Three-dimensional (3D) printing is a powerful manufacturing tool for making 3D structures with well-defined architectures for a wide range of applications. The field of tissue engineering has also adopted this technology to fabricate scaffolds for tissue regeneration. The ability to control architecture of scaffolds, e.g. matching anatomical shapes and having defined pore size, has since been improved significantly. However, the material surface of these scaffolds is smooth and does not resemble that found in natural extracellular matrix (ECM), in particular, the nanofibrous morphology of collagen...
December 13, 2017: Biofabrication
https://www.readbyqxmd.com/read/29235442/the-effect-of-rna-stiffness-on-the-self-assembly-of-virus-particles
#20
Siyu Li, Gonca Erdemci-Tandogan, Paul van der Schoot, Roya Zandi
Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between a ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins...
December 13, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
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