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https://www.readbyqxmd.com/read/28340512/activation-mechanisms-of-%C3%AE-v%C3%AE-3-integrin-by-binding-to-fibronectin-a-computational-study
#1
Lingyun Wang, Di Pan, Qi Yan, Yuhua Song
Integrin αVβ3 plays an important role in regulating cellular activities and in human diseases. Although the structure of αVβ3 has been studied by crystallography and electron microscopy, the detailed activation mechanism of integrin αVβ3 induced by fibronectin (Fn) remains unclear. In this study, we investigated the conformational and dynamical motion changes of Mn(2+) -bound integrin αVβ3 by binding to Fn with molecular dynamics simulations. Results showed that Fn binding to integrin αVβ3 caused the changes of the conformational flexibility of αVβ3 domains, the essential mode of motion for the domains of αV subunit and β3 subunit and the degrees of correlated motion of residues between the domains of αV subunit and β3 subunit of integrin αVβ3...
March 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28340510/the-diverse-family-of-mmpl-transporters-in-mycobacteria-from-regulation-to-antimicrobial-developments
#2
REVIEW
Albertus Viljoen, Violaine Dubois, Fabienne Girard-Misguich, Mickael Blaise, Jean-Louis Herrmann, Laurent Kremer
Mycobacterial genomes contain large sets of loci encoding membrane proteins that belong to a family of multidrug resistance pumps designated Resistance-Nodulation-Cell Division (RND) permeases. Mycobacterial membrane protein Large (MmpL) transporters represent a subclass of RND transporters known to participate in the export of lipid components across the cell envelope. These surface-exposed lipids with unusual structures play key roles in the physiology of mycobacteria and/or can act as virulence factors and immunomodulators...
March 24, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28340487/microrna-4739-regulates-osteogenic-and-adipocytic-differentiation-of-immortalized-human-bone-marrow-stromal-cells-via-targeting-lrp3
#3
Mona Elsafadi, Muthurangan Manikandan, Nehad M Alajez, Rimi Hamam, Raed Abu Dawud, Abdullah Aldahmash, Zafar Iqbal, Musaad Alfayez, Moustapha Kassem, Amer Mahmood
Understanding the regulatory networks underlying lineage differentiation and fate determination of human bone marrow stromal cells (hBMSC) is a prerequisite for their therapeutic use. The goal of the current study was to unravel the novel role of the low-density lipoprotein receptor-related protein 3 (LRP3) in regulating the osteogenic and adipogenic differentiation of immortalized hBMSCs. Gene expression profiling revealed significantly higher LRP3 levels in the highly osteogenic hBMSC clone imCL1 than in the less osteogenic clone imCL2, as well as a significant upregulation of LRP3 during the osteogenic induction of the imCL1 clone...
March 8, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28340484/engineering-of-layered-lipid-encapsulated-drug-nanoparticles-through-spray-drying
#4
Mahak Sapra, Y S Mayya, Chandra Venkataraman
Drug-containing nanoparticles have been synthesized through the spray-drying of submicron droplet aerosols by using matrix materials such as lipids and biopolymers. Understanding layer formation in composite nanoparticles is essential for the appropriate engineering of particle substructures. The present study developed a droplet-shrinkage model for predicting the solid-phase formation of two non-volatile solutes-stearic acid lipid and a set of drugs, by considering molecular volume and solubility. Nanoparticle formation was simulated to define the parameter space of material properties and process conditions for the formation of a layered structure with the preferential accumulation of the lipid in the outer layer...
March 18, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28340459/transcriptional-profiling-of-porcine-granulosa-cells-exposed-to-2-3-7-8-tetrachlorodibenzo-p-dioxin
#5
Agnieszka Sadowska, Anna Nynca, Monika Ruszkowska, Lukasz Paukszto, Kamil Myszczynski, Karina Orlowska, Sylwia Swigonska, Tomasz Molcan, Jan P Jastrzebski, Renata E Ciereszko
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical compound contaminating the environment. An exposure of living organisms to TCDD may result in numerous disorders, including reproductive pathologies. The aim of the current study was to examine the effects of TCDD on the transcriptome of porcine granulosa cell line AVG-16. By employing next-generation sequencing (NGS) we aimed to identify genes potentially involved in the mechanism of TCDD action and toxicity in porcine granulosa cells...
March 16, 2017: Chemosphere
https://www.readbyqxmd.com/read/28340427/identification-and-characterization-of-a-%C3%AE-defensin-gene-involved-in-the-immune-defense-response-of-channel-catfish-ictalurus-punctatus
#6
Jieyao Zhu, Hong Wang, Jun Wang, Xingli Wang, Shuang Peng, Yi Geng, Kaiyu Wang, Pin Ouyang, Zhiqiong Li, Xiaoli Huang, Defang Chen
Antimicrobial peptides are small peptides that play important roles in a host's innate immune response. As an important antimicrobial peptide, β-defensin widely distribute in mammals, insects and plants with broad-spectrum antimicrobial activity. In this study, the β-defensin gene of the channel catfish, Ictalurus punctatus, was cloned, sequenced, and subjected to a bioinformatic analysis. The β-defensin gene of the channel catfish contains three exons and two introns, and encodes a precursor peptide consisting of two domains: a signal peptide of 24 amino acid residues and a mature peptide of 43 amino acid residues...
March 21, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28340426/porcine-parvovirus-induces-activation-of-nf-%C3%AE%C2%BAb-signaling-pathways-in-pk-15-cells-mediated-by-toll-like-receptors
#7
Liyan Cao, Jianfei Chen, Yanwu Wei, Hongyan Shi, Xin Zhang, Jing Yuan, Da Shi, Jianbo Liu, Xiangdong Zhu, Xin Wang, Shangjin Cui, Li Feng
Porcine parvovirus (PPV) is a pathogenic factor that primarily induces severe reproductive failure of pregnant swine, which results in extensive losses to the swine industry worldwide. In this study, a potential mechanism of PPV-induced activation of the nuclear transcription factor-kappaB (NF-κB) by infection in porcine kidney cells (PK-15) was elucidated for the first time. The subcellular localization of p65 analyzed by immunofluorescence assay (IFA) showed that PPV infection induced p65 translocation from the cytoplasm to the nucleus...
March 21, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28340417/interfacial-interactions-between-skeletonema-costatum-extracellular-organic-matter-and-metal-oxides-implications-for-ceramic-membrane-filtration
#8
Noor Zaouri, Leonardo Gutierrez, Laure Dramas, Daniel Garces, Jean-Philippe Croue
In the current study, the interfacial interactions between the high molecular weight (HMW) compounds of Skeletonema costatum (SKC) extracellular organic matter (EOM) and ZrO2 or Al2O3, were investigated by atomic force microscopy (AFM). HMW SKC-EOM was rigorously characterized and described as a hydrophilic organic compound mainly comprised of polysaccharide-like structures. Lipids and proteins were also observed, although in lower abundance. HMW SKC-EOM displayed attractive forces during approaching (i.e., leading to jump-to-contact events) and adhesion forces during retracting regime to both metal oxides at all solution conditions tested, where electrostatics and hydrogen bonding were suggested as dominant interacting mechanisms...
March 21, 2017: Water Research
https://www.readbyqxmd.com/read/28340413/design-synthesis-and-biological-evaluation-of-novel-coumarin-based-benzamides-as-potent-histone-deacetylase-inhibitors-and-anticancer-agents
#9
Tooba Abdizadeh, Mohammad Reza Kalani, Khalil Abnous, Zahra Tayarani-Najaran, Bibi Zahra Khashyarmanesh, Rahman Abdizadeh, Razieh Ghodsi, Farzin Hadizadeh
Histone deacetylases (HDACs) are attractive therapeutic targets for the treatment of cancer and other diseases. It has four classes (I-IV), among them especially class I isozyme are involved in promoting tumor cells proliferation, angiogenesis, differentiation, invasion and metastasis and also viable targets for cancer therapeutics. A novel series of coumarin-based benzamides was designed and synthesized as HDAC inhibitors. The cytotoxic activity of the synthesized compounds (8a-u) was evaluated against six human cancer cell lines including HCT116, A2780, MCF7, PC3, HL60 and A549 and a single normal cell line (Huvec)...
March 18, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28340411/synthesis-and-biological-evaluation-of-novel-chalcone-derivatives-as-a-new-class-of-microtubule-destabilizing-agents
#10
Xiaochao Huang, Rizhen Huang, Lingxue Li, Shaohua Gou, Hengshan Wang
A series of novel chalcone derivatives were designed and synthesized as potential antitumor agents. Structures of target molecules were confirmed by (1)H NMR, (13)C NMR and HR-MS, and evaluated for their in vitro anti-proliferative activities using MTT assay. Among them, compound 12k displayed potent activity against the test tumor cell lines including multidrug resistant human cancer lines, with the IC50 values ranged from 3.75 to 8.42 μM. In addition, compound 12k was found to induce apoptosis in NCI-H460 cells via the mitochondrial pathway, including an increase of the ROS level, loss of mitochondrial membrane potential, release of cytochrome c, down-regulation of Bcl-2, up-regulation of Bax, activation of caspase-9 and caspase-3, respectively...
March 18, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28340400/pharmacoinformatics-exploration-of-polyphenol-oxidases-leading-to-novel-inhibitors-by-virtual-screening-and-molecular-dynamic-simulation-study
#11
Mubashir Hassan, Qamar Abbas, Zaman Ashraf, Ahmed A Moustafa, Sung-Yum Seo
Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis...
March 15, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28340398/proteomics-analysis-of-maize-zea-mays-l-grain-based-on-itraq-reveals-molecular-mechanisms-of-poor-grain-filling-in-inferior-grains
#12
Tao Yu, Geng Li, Peng Liu, Shuting Dong, Jiwang Zhang, Bin Zhao
In maize, inferior grains (IG) located on the upper part of the ear have poor grain filling process compared to superior grains (SG) located on the middle and lower parts of the ear. This difference limits satisfactory yield and quality; however, the underlying molecular mechanisms remain unknown. Here, using the isobaric tag for relative and absolute quantification (iTRAQ) technology, the proteomes of IG and SG during early and middle grain filling stages were investigated. In total, 4720 proteins were identified in maize grain and 305 differentially accumulated proteins (DiAPs) were detected between IG and SG...
March 11, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28340387/an-exploration-of-the-effect-and-interaction-mechanism-of-bisphenol-a-on-waste-sludge-hydrolysis-with-multi-spectra-isothermal-titration-microcalorimetry-and-molecule-docking
#13
Guangying Hou, Rui Zhang, Xiaoyan Hao, Chunguang Liu
An increasing amount of bisphenol A (BPA) is being produced and used, then discharged into sewage treatment plants and accumulated in sludge or soil, when the sludge is used as fertilizer. Accumulation of BPA in sludge or soil causes poisoning to the enzyme, which affects the biological treatment of sludge and the circulation and conversion of materials in soil. In this research, effect of BPA on sludge hydrolysis is studied from the respect of concentration and components of soluble organic matter in sludge, using three-dimensional fluorescence spectra...
March 10, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28340381/studying-the-adsorption-of-dna-nanostructures-on-graphene-in-the-aqueous-phase-using-molecular-dynamic-simulations
#14
Jixue Sun, Yang Li, Jianping Lin
DNA nanostructures can undergo large structural fluctuations and deviate from their intended configurations. In this work, two model DNA nanostructures (i.e., Nan and Kai) were designed based on the shape of the two Chinese characters of the name of Nankai University, and additional single-stranded DNA fragments were added to interact with graphene. During four 50-ns molecular dynamic simulations in aqueous solution, the DNA nanostructures adsorbed onto graphene demonstrated more stable conformations with lower root mean square deviations and smaller coordinate changes in the z-axis direction than the DNA nanostructures that were not adsorbed onto graphene...
March 9, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28340379/knockdown-of-ska1-gene-inhibits-cell-proliferation-and-metastasis-in-human-adenoid-cystic-carcinoma
#15
Li-Juan Zhao, Hong-Li Yang, Ke-Yi Li, Yue-Hua Gao, Kai Dong, Zhong-Hao Liu, Le-Xin Wang, Bin Zhang
The spindle and kinetochore-associated complex subunit 1(SKA1) is a newly discovered gene, which has been associated with mitosis and tumorigenesis. However, its role insalivary adenoid cystic carcinoma (SACC) is still unknown, and the invasive and metastatic mechanism in SACC is still unclear. To explore the molecular mechanism of SKA1 in the process of malignant proliferation and metastasis in adenoid cystic cancer (ACC) cells, we employed lentivirus-mediated short hairpin RNA to knockdown SKA1 in SACC-83 cells...
March 21, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28340368/synthesis-molecular-docking-antimycobacterial-and-antimicrobial-evaluation-of-new-pyrrolo-3-2-c-pyridine-mannich-bases
#16
Gilish Jose, Tholappanavara H Suresha Kumara, Haliwana B V Sowmya, Dharmarajan Sriram, Tayur N Guru Row, Amar A Hosamani, Sunil S More, Bhavya Janardhan, B G Harish, Sandeep Telkar, Yalegara Siddappa Ravikumar
In this report, we describe the synthesis and biological evaluation of a new series of pyrrolo[3,2-c]pyridine Mannich bases (7a-v). The Mannich bases were obtained in good yields by one-pot three component condensation of pyrrolo[3,2-c]pyridine scaffold (6a-c) with secondary amines and excess of formaldehyde solution in AcOH. The chemical structures of the compounds were characterized by (1)H NMR, (13)C NMR, LC/MS and elemental analysis. Single crystal X-ray diffraction has been recorded for compound 7k ([C23H29ClN4](+2), H2O)...
March 16, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28340358/lysosomal-rupture-induced-by-structurally-distinct-chitosans-either-promotes-a-type-1-ifn-response-or-activates-the-inflammasome-in-macrophages
#17
David Fong, Pascal Grégoire-Gélinas, Alexandre P Cheng, Tal Mezheritsky, Marc Lavertu, Sachiko Sato, Caroline D Hoemann
Chitosan is a family of glucosamine and N-acetyl glucosamine polysaccharides with poorly understood immune modulating properties. Here, functional U937 macrophage responses were analyzed in response to a novel library of twenty chitosans with controlled degree of deacetylation (DDA, 60-98%), molecular weight (1 to >100 kDa), and acetylation pattern (block vs. random). Specific chitosan preparations (10 or 190 kDa 80% block DDA and 3, 5, or 10 kDa 98% DDA) either induced macrophages to release CXCL10 and IL-1ra at 5-50 μg/mL, or activated the inflammasome to release IL-1β and PGE2 at 50-150 μg/mL...
March 15, 2017: Biomaterials
https://www.readbyqxmd.com/read/28340354/mechanism-of-substrate-translocation-in-an-alternating-access-transporter
#18
Naomi R Latorraca, Nathan M Fastman, A J Venkatakrishnan, Wolf B Frommer, Ron O Dror, Liang Feng
Transporters shuttle molecules across cell membranes by alternating among distinct conformational states. Fundamental questions remain about how transporters transition between states and how such structural rearrangements regulate substrate translocation. Here, we capture the translocation process by crystallography and unguided molecular dynamics simulations, providing an atomic-level description of alternating access transport. Simulations of a SWEET-family transporter initiated from an outward-open, glucose-bound structure reported here spontaneously adopt occluded and inward-open conformations...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28340353/molecular-structure-of-the-human-cftr-ion-channel
#19
Fangyu Liu, Zhe Zhang, László Csanády, David C Gadsby, Jue Chen
The cystic fibrosis transmembrane conductance regulator (CFTR) is an ATP-binding cassette (ABC) transporter that uniquely functions as an ion channel. Here, we present a 3.9 Å structure of dephosphorylated human CFTR without nucleotides, determined by electron cryomicroscopy (cryo-EM). Close resemblance of this human CFTR structure to zebrafish CFTR under identical conditions reinforces its relevance for understanding CFTR function. The human CFTR structure reveals a previously unresolved helix belonging to the R domain docked inside the intracellular vestibule, precluding channel opening...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28340349/structure-reveals-mechanisms-of-viral-suppressors-that-intercept-a-crispr-rna-guided-surveillance-complex
#20
Saikat Chowdhury, Joshua Carter, MaryClare F Rollins, Sarah M Golden, Ryan N Jackson, Connor Hoffmann, Lyn'Al Nosaka, Joseph Bondy-Denomy, Karen L Maxwell, Alan R Davidson, Elizabeth R Fischer, Gabriel C Lander, Blake Wiedenheft
Genetic conflict between viruses and their hosts drives evolution and genetic innovation. Prokaryotes evolved CRISPR-mediated adaptive immune systems for protection from viral infection, and viruses have evolved diverse anti-CRISPR (Acr) proteins that subvert these immune systems. The adaptive immune system in Pseudomonas aeruginosa (type I-F) relies on a 350 kDa CRISPR RNA (crRNA)-guided surveillance complex (Csy complex) to bind foreign DNA and recruit a trans-acting nuclease for target degradation. Here, we report the cryo-electron microscopy (cryo-EM) structure of the Csy complex bound to two different Acr proteins, AcrF1 and AcrF2, at an average resolution of 3...
March 23, 2017: Cell
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