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https://www.readbyqxmd.com/read/28214775/role-of-c-di-gmp-in-anammox-aggregation-and-systematic-analysis-of-its-turnover-protein-in-candidatus-jettenia-caeni
#1
Yongzhao Guo, Sitong Liu, Xi Tang, Fenglin Yang
The anaerobic ammonium oxidation (anammox) process has been recognized as a promising sewage treatment approach. Considering the susceptibility, it is meaningful to study the behaviors of anammox bacteria under the unfavorable conditions. Here, we found that anammox bacteria more probably tended to aggregation by the regulation of c-di-GMP against the unfavorable environmental stresses (low temperature, aerobic condition and low pH). Further using multiple protein sequence alignment, we systematically examined the functionality of thirteen genes encoding putative c-di-GMP metabolic enzymes in anammox organism Candidatus Jettenia caeni, revealing most of the predicted enzymes were predicted to be active...
February 12, 2017: Water Research
https://www.readbyqxmd.com/read/28214753/structural-and-functional-insights-into-corrinoid-iron-sulfur-protein-from-human-pathogen-clostridium-difficile
#2
Yaozhu Wei, Xiaofei Zhu, Sixue Zhang, Xiangshi Tan
The human pathogen Clostridium difficile infection (CDI) is one of the most important healthcare-associated infections. The Wood-Ljungdahl pathway, which is responsible for Acetyl-CoA biosynthesis, is essential for the survival of the pathogen and is absent in humans. The key proteins and enzymes involved in the pathway are attractive targets for the treatment of CDI. Corrinoid iron-sulfur protein (CoFeSP) is a key protein and acts as a methyl transformer in the Wood-Ljungdahl pathway. In this study, CoFeSP from Clostridium difficile (CoFeSPCd) was cloned, expressed in E...
February 13, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28213521/signalling-adaptor-shcd-suppresses-erk-phosphorylation-distal-to-the-ret-and-trk-neurotrophic-receptors
#3
Melanie K B Wills, Ava Keyvani Chahi, Hayley R Lau, Manali Tilak, Brianna Guild, Laura A New, Peihua Lu, Keévin Jacquet, Susan O Meakin, Nicolas Bisson, Nina Jones
Proteins of the Shc family are typically involved in signal transduction events involving Ras/MAPK and PI3K/Akt pathways. In the nervous system, they function proximal to the neurotrophic factors that regulate cell survival, differentiation, and neuron-specific characteristics. The least-characterized homolog, ShcD, is robustly expressed in the developing and mature nervous system, but its contributions to neural cell circuitry are largely uncharted. We now report that ShcD binds to active Ret, TrkA, and TrkB neurotrophic factor receptors predominantly via its phosphotyrosine binding (PTB) domain...
February 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28213174/evidence-of-the-presence-of-a-calmodulin-sensitive-plasma-membrane-ca-2-atpase-in-trypanosoma-equiperdum
#4
María Carolina Pérez-Gordones, José Rubén Ramírez-Iglesias, Vincenza Cervino, Graciela L Uzcanga, Gustavo Benaim, Marta Mendoza
Trypanosoma equiperdum belongs to the subgenus Trypanozoon, which has a significant socio-economic impact by limiting animal protein productivity worldwide. Proteins involved in the intracellular Ca(2+) regulation are prospective chemotherapeutic targets since several drugs used in experimental treatment against trypanosomatids exert their action through the disruption of the parasite intracellular Ca(2+) homeostasis. Therefore, the plasma membrane Ca(2+)-ATPase (PMCA) is considered as a potential drug target...
February 14, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28212383/novel-molecular-structural-and-evolutionary-characteristics-of-the-phosphoketolases-from-bifidobacteria-and-coriobacteriales
#5
Radhey S Gupta, Anish Nanda, Bijendra Khadka
Members from the order Bifidobacteriales, which include many species exhibiting health promoting effects, differ from all other organisms in using a unique pathway for carbohydrate metabolism, known as the "bifid shunt", which utilizes the enzyme phosphoketolase (PK) to carry out the phosphorolysis of both fructose-6-phosphate (F6P) and xylulose-5-phosphate (X5P). In contrast to bifidobacteria, the PKs found in other organisms (referred to XPK) are able to metabolize primarily X5P and show very little activity towards F6P...
2017: PloS One
https://www.readbyqxmd.com/read/28207811/accelerated-flexible-protein-ligand-docking-using-hamiltonian-replica-exchange-with-a-repulsive-biasing-potential
#6
Katja Ostermeir, Martin Zacharias
A molecular dynamics replica exchange based method has been developed that allows rapid identification of putative ligand binding sites on the surface of biomolecules. The approach employs a set of ambiguity restraints in replica simulations between receptor and ligand that allow close contacts in the reference replica but promotes transient dissociation in higher replicas. This avoids long-lived trapping of the ligand or partner proteins at nonspecific, sticky, sites on the receptor molecule and results in accelerated exploration of the possible binding regions...
2017: PloS One
https://www.readbyqxmd.com/read/28206754/high-quality-dataset-of-protein-bound-ligand-conformations-and-its-application-to-benchmarking-conformer-ensemble-generators
#7
Nils-Ole Friedrich, Agnes Meyder, Christina de Bruyn Kops, Kai Sommer, Florian Flachsenberg, Matthias Rarey, Johannes Kirchmair
We developed a cheminformatics pipeline for the fully automated selection and extraction of high-quality protein-bound ligand conformations from X-ray structural data. The pipeline evaluates the validity and accuracy of the 3D structures of small molecules according to multiple criteria, including their fit to the electron density and their physicochemical and structural properties. Using this approach, we compiled two high-quality datasets from the Protein Data Bank (PDB): a comprehensive dataset and a diversified subset of 4626 and 2912 structures, respectively...
February 16, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28205401/computer-aided-drug-design-to-explore-cyclodextrin-therapeutics-and-biomedical-applications
#8
Azizeh Abdolmaleki, Fatemeh Ghasemi, Jahan B Ghasemi
Cyclodextrin (CD) is a subset of the macrocyclic structural class, which is an important class of small organic agents that are useful functional excipients. They have wide range application possibilities in different fields of sciences such as material preparation, medicine, analytical chemistry, and separation processes. They are used widely in pharmaceutical formulations and drug delivery for increasing the water solubility of low soluble drugs and drug candidates. Due to the ring structure, they behave differently than smaller molecules and may be capable of hitting new classes of targets...
February 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28198010/phenolic-1-3-diketones-attenuate-lipopolysaccharide-induced-inflammatory-response-by-an-alternative-magnesium-mediated-mechanism
#9
Morena Zusso, Giulia Mercanti, Federica Belluti, Rita Maria Concetta Di Martino, Andrea Pagetta, Carla Marinelli, Paola Brun, Eugenio Ragazzi, Rita Lo, Stefano Stifani, Pietro Giusti, Stefano Moro
BACKGROUND AND PURPOSE: Toll-like receptor 4 (TLR4) plays a key role in the induction of inflammatory responses both in peripheral organs and the CNS. Curcumin exerts anti-inflammatory functions by interfering with LPS-induced TLR4-myeloid differentiation protein-2 (MD-2) dimerization and suppressing pro-inflammatory mediator release. However, the inhibitory mechanism of curcumin remains to be defined. EXPERIMENTAL APPROACH: Binding of bis-demethoxycurcumin (GG6) and its cyclized pyrazole analogue (GG9), which lacks the 1,3-dicarbonyl function, to TLR4-MD-2 was determined using molecular docking simulations...
February 15, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28197415/pharmacoinformatics-adaptive-evolution-and-elucidation-of-six-novel-compounds-for-schizophrenia-treatment-by-targeting-daoa-g72-isoforms
#10
Sheikh Arslan Sehgal
Studies on Schizophrenia so far reveal a complex picture of neurological malfunctioning reported to be strongly associated with DAOA. Detailed sequence analyses proved DAOA as a primate specific gene having conserved gene desert region on both upstream and downstream region. The analyses of 10 MB chromosomal region of primates, birds, rodents, and reptiles having DAOA evidenced the conserved part in primates and in the rest of species, while DAOA is only present in primates. DAOA has four isoforms having one interaction partner DAO...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28196708/design-synthesis-and-biological-evaluation-of-2-4-disubstituted-oxazole-derivatives-as-potential-pde4-inhibitors
#11
Ya-Sheng Li, De-Kun Hu, Dong-Sheng Zhao, Xing-Yu Liu, Hong-Wei Jin, Gao-Peng Song, Zi-Ning Cui, Lian-Hui Zhang
In this study, a series of pyrazole derivatives containing 4-phenyl-2-oxazole moiety were designed and synthesized in a concise way, some of which exhibited considerable inhibitory activity against PDE4B and blockade of LPS-induced TNF-α release. Compound 4c displayed the strongest inhibition activity (IC50=1.6±0.4μM) and good selectivity against PDE4B. Meanwhile, compound 4c showed good in vivo activity in animal models of asthma/COPD and sepsis induced by LPS. The primary structure-activity relationship study showed the 3,5-dimethylpyrazole residue was essential for the bioactivity, and the substituted group R1 at the benzene ring also affected the activity...
February 3, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28196677/molecular-modeling-docking-and-dynamics-simulations-of-the-dioclea-lasiophylla-mart-ex-benth-seed-lectin-an-edematogenic-and-hypernociceptive-protein
#12
Vanir Reis Pinto-Junior, Vinicius Jose Silva Osterne, Mayara Queiroz Santiago, Claudia Figueiredo Lossio, Celso Shiniti Nagano, Cintia Renata Costa Rocha, Jessica Catarine Frutuoso Nascimento, Francisco Lucas Faustino Nascimento, Ivanice Bezerra Silva, Antonia Simoni Oliveira, Jorge Luis Almeida Correia, Rodrigo Bainy Leal, Ana Maria Sampaio Assreuy, Benildo Sousa Cavada, Kyria Santiago Nascimento
Lectins are proteins, or glycoproteins, capable of reversibly binding to specific mono- or oligosaccharides via a noncatalytic domain. The Diocleinae subtribe presents lectins with high structural similarity, but different effects based on biological activity assays. This variability results from small structural differences. Therefore, in this context, the present study aimed to perform a structural analysis of the lectin from Dioclea lasiophylla Mart. ex Benth seeds (DlyL) and evaluate its inflammatory effect...
February 11, 2017: Biochimie
https://www.readbyqxmd.com/read/28196116/the-scoring-bias-in-reverse-docking-and-the-score-normalization-strategy-to-improve-success-rate-of-target-fishing
#13
Qiyao Luo, Liang Zhao, Jianxing Hu, Hongwei Jin, Zhenming Liu, Liangren Zhang
Target fishing often relies on the use of reverse docking to identify potential target proteins of ligands from protein database. The limitation of reverse docking is the accuracy of current scoring funtions used to distinguish true target from non-target proteins. Many contemporary scoring functions are designed for the virtual screening of small molecules without special optimization for reverse docking, which would be easily influenced by the properties of protein pockets, resulting in scoring bias to the proteins with certain properties...
2017: PloS One
https://www.readbyqxmd.com/read/28195474/improving-screening-efficiency-through-iterative-screening-using-docking-and-conformal-prediction
#14
Fredrik Svensson, Ulf Norinder, Andreas Bender
High throughput screening, where thousands of molecules rapidly can be assessed for activity against a protein, has been the dominating approach in drug discovery for many years. However, these methods are costly and require much time and effort. In order to suggest an improvement to this situation we, in this study, apply an iterative screening process where an initial set of compounds are selected for screening based on molecular docking. The outcome of the initial screen is then used to classify the remaining compounds through a conformal predictor...
February 14, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28195395/heterologous-expression-of-helicoverpa-armigera-cytochrome-p450-cyp6b7-in-pichia-pastoris-and-interactions-of-cyp6b7-with-insecticides
#15
Chunqing Zhao, Genmiao Song, Hongxia Duan, Tao Tang, Chen Wang, Lihong Qiu
BACKGROUND: Previous studies indicated that constitutive overexpression of cytochrome P450 CYP6B7 was involved in fenvalerate resistance in Helicoverpa armigera. In this study, the CYP6B7 gene from H. armigera (namely HaCYP6B7), was heterologously expressed in Pichia pastoris GS115. A vector pPICZA-HaCYP6B7 was constructed and transformed into P. pastoris GS115, the transformant of pPICZA-HaCYP6B7-GS115 was then cultured and induced by 1% (v/v) methanol and the heterologous expression of HaCYP6B7 protein in P...
February 13, 2017: Pest Management Science
https://www.readbyqxmd.com/read/28194576/design-synthesis-and-antibacterial-activities-of-novel-heterocyclic-arylsulphonamide-derivatives
#16
Anuradha Singh, Ritika Srivastava, Ramendra K Singh
Design, synthesis, and antibacterial activities of a series of arylsulphonamide derivatives as probable peptide deformylase (PDF) inhibitors have been discussed. Compounds have been designed following Lipinski's rule and after docking into the active site of PDF protein (PDB code: 1G2A) synthesized later on. Furthermore, to assess their antibacterial activity, screening of the compound was done in vitro conditions against Gram-positive and Gram-negative bacterial strains. In silico, studies revealed these compounds as potential antibacterial agents and this fact was also supported by their prominent scoring functions...
February 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28194462/designing-an-efficient-multi-epitope-oral-vaccine-against-helicobacter-pylori-using-immunoinformatics-and-structural-vaccinology-approaches
#17
Navid Nezafat, Mahboobeh Eslami, Manica Negahdaripour, Mohammad Reza Rahbar, Younes Ghasemi
Helicobacter pylori is the cunning bacterium that can live in the stomachs of many people without any symptoms, but gradually can lead to gastric cancer. Due to various obstacles, which are related to anti-H. pylori antibiotic therapy, recently developing an anti-H. pylori vaccine has attracted more attention. In this study, different immunoinformatics and computational vaccinology approaches were employed to design an efficient multi-epitope oral vaccine against H. pylori. Our multi-epitope vaccine is composed of heat labile enterotoxin IIc B (LT-IIc) that is used as a mucosal adjuvant to enhance vaccine immunogenicity for oral immunization, cartilage oligomeric matrix protein (COMP) to increase vaccine stability in acidic pH of gut, one experimentally protective antigen, OipA, and two hypothetical protective antigens, HP0487 and HP0906, and "CTGKSC" peptide motif that target epithelial microfold cells (M cells) to enhance vaccine uptake from the gut barrier...
February 14, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28193861/galectin-3-directs-antimicrobial-guanylate-binding-proteins-to-vacuoles-furnished-with-bacterial-secretion-systems
#18
Eric M Feeley, Danielle M Pilla-Moffett, Erin E Zwack, Anthony S Piro, Ryan Finethy, Joseph P Kolb, Jennifer Martinez, Igor E Brodsky, Jörn Coers
Many invasive bacteria establish pathogen-containing vacuoles (PVs) as intracellular niches for microbial growth. Immunity to these infections is dependent on the ability of host cells to recognize PVs as targets for host defense. The delivery of several host defense proteins to PVs is controlled by IFN-inducible guanylate binding proteins (GBPs), which themselves dock to PVs through poorly characterized mechanisms. Here, we demonstrate that GBPs detect the presence of bacterial protein secretion systems as "patterns of pathogenesis" associated with PVs...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193857/mass-spectrometry-based-cross-linking-study-shows-that-the-psb28-protein-binds-to-cytochrome-b559-in-photosystem-ii
#19
Daniel A Weisz, Haijun Liu, Hao Zhang, Sundarapandian Thangapandian, Emad Tajkhorshid, Michael L Gross, Himadri B Pakrasi
Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193765/a-novel-chemical-inhibitor-of-aba-signaling-targets-all-aba-receptors
#20
Ya-Jin Ye, Lijuan Zhou, Xue Liu, Hao Liu, Deqiang Li, Minjie Cao, Haifeng Chen, Lin Xu, Jiankang Zhu, Yang Zhao
Abscisic acid (ABA), the most important stress-induced phytohormone, regulates seed dormancy, germination, plant senescence and abiotic stress response. ABA signaling is repressed by protein phosphatases 2C (PP2Cs), then ABA binds to its receptor of the PYR/PYL/RCAR family, which in turn inhibits PP2Cs and activates downstream ABA signaling. The agonist/antagonist of ABA receptors have the potential to unveil the ABA signaling machinery and to become lead compounds for agrochemicals, however, up to now, no broad-spectrum antagonists of ABA receptors blocking all PYR/PYL-PP2C interactions have been identified...
February 13, 2017: Plant Physiology
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