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https://www.readbyqxmd.com/read/28651230/comparative-proteomic-and-metabolomic-studies-between-prunus-persica-genotypes-resistant-and-susceptible-to-taphrina-deformans-suggest-a-molecular-basis-of-resistance
#1
Camila Goldy, Laura A Svetaz, Claudia A Bustamante, Marco Allegrini, Gabriel H Valentini, María F Drincovich, Alisdair R Fernie, María V Lara
The worldwide-distributed leaf peach curl disease is caused by the biotroph Taphrina deformans. To characterize the plant-fungus interaction, resistant and susceptible Prunus persica genotypes grown in the orchard were studied. Asymptomatic leaves were tested for fungal presence. In all resistant leaves analyzed the fungus was not detected. Conversely, leaves from the susceptible genotype were categorized according to the presence or absence of the pathogen. Comparative metabolomic analysis disclosed the metabolite composition associated with resistant and susceptible interactions, and of compounds involved in fungal growth inhibition such as chlorogenic acid, whose in vitro antifungal activity was verified in this work...
June 17, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28651174/label-free-chronopotentiometric-glycoprofiling-of-prostate-specific-antigen-using-sialic-acid-recognizing-lectins
#2
Stefan Belicky, Hana Černocká, Tomas Bertok, Alena Holazova, Kamila Réblová, Emil Paleček, Jan Tkac, Veronika Ostatná
In recent decades, it has become clear that most of human proteins are glycosylated and that protein glycosylation plays an important role in health and diseases. At present, simple, fast and inexpensive methods are sought for clinical applications and particularly for improved diagnostics of various diseases, including cancer. We propose a label- and reagent-free electrochemical method based on chronopotentiometric stripping (CPS) analysis and a hanging mercury drop electrode for the detection of interaction of sialylated protein biomarker a prostate specific antigen (PSA) with two important lectins: Sambucus nigra agglutinin (SNA) and Maackia amurensis agglutinin (MAA)...
June 19, 2017: Bioelectrochemistry
https://www.readbyqxmd.com/read/28651144/improved-anticancer-effects-of-albumin-bound-paclitaxel-nanoparticle-via-augmentation-of-epr-effect-and-albumin-protein-interactions-using-s-nitrosated-human-serum-albumin-dimer
#3
Ryo Kinoshita, Yu Ishima, Victor T G Chuang, Hideaki Nakamura, Jun Fang, Hiroshi Watanabe, Taro Shimizu, Keiichiro Okuhira, Tatsuhiro Ishida, Hiroshi Maeda, Masaki Otagiri, Toru Maruyama
In the latest trend of anticancer chemotherapy research, there were many macromolecular anticancer drugs developed based on enhanced permeability and retention (EPR) effect, such as albumin bound paclitaxel nanoparticle (nab- PTX, also called Abraxane(®)). However, cancers with low vascular permeability posed a challenge for these EPR based therapeutic systems. Augmenting the intrinsic EPR effect with an intrinsic vascular modulator such as nitric oxide (NO) could be a promising strategy. S-nitrosated human serum albumin dimer (SNO-HSA Dimer) shown promising activity previously was evaluated for the synergistic effect when used as a pretreatment agent in nab-PTX therapy against various tumor models...
June 22, 2017: Biomaterials
https://www.readbyqxmd.com/read/28651078/leuconostoc-mesenteroides-and-leuconostoc-pseudomesenteroides-bacteriophages-genomics-and-cross-species-host-ranges
#4
Silvina A Pujato, Daniela M Guglielmotti, Manuel Martínez-García, Andrea Quiberoni, Francisco J M Mojica
Unveiling virus-host interactions are relevant for understanding the biology and evolution of microbes globally, but in particular, it has also a paramount impact on the manufacture of fermented dairy products. In this study, we aim at characterizing phages infecting the commonly used heterofermentative Leuconostoc spp. on the basis of host range patterns and genome analysis. Host range of six Leuconostoc phages was investigated using three methods (efficiency of plaquing, spot and turbidity tests) against Ln...
June 12, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28651056/significantly-improved-protein-folding-thermodynamics-using-a-dispersion-corrected-water-model-and-a-new-residue-specific-force-field
#5
Hao-Nan Wu, Fan Jiang, Yun-Dong Wu
An accurate potential energy model is crucial for biomolecular simulations. Despite many recent improvements of classical protein force fields, there are remaining key issues: much weaker temperature-dependence of folding/unfolding equilibrium, and overly collapsed unfolded or disordered states. For the later problem, a new water model (TIP4P-D) has been proposed to correct the significantly underestimated water dispersion interactions. Here, using TIP4P-D, we reveal problems in current force fields through failures in folding model systems (a polyalanine peptide, Trp-cage and the GB1 hairpin)...
June 26, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28651041/interaction-of-vivo-acac-2-with-human-serum-transferrin-and-albumin
#6
João Costa Pessoa, Isabel Correia, Ielyzaveta Chorna, Isabel Cavaco, Somnath Roy, Maxim L Kuznetsov, Nádia Ribeiro, Gonçalo Justino, Fernanda Marques, Teresa Santos Silva, Marino Santos, Hugo M Santos, José L Capelo, James Doutch
[VO(acac)2] is a remarkable vanadium compound and has potential as a therapeutic drug. It is important to clarify how it is transported in blood, but the reports addressing its binding to serum proteins have been contradictory. We use several spectroscopic and mass spectrometric techniques (ESI and MALDI-TOF), small-angle X-ray scattering and size exclusion chromatography (SEC) to characterize solutions containing [VO(acac)2] and either human serum apotransferrin (apoHTF) or albumin (HSA). DFT and modeling protein calculations are carried out to disclose the type of binding to apoHTF...
June 26, 2017: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/28651026/binding-of-human-plasminogen-and-high-molecular-mass-kininogen-by-cell-surface-exposed-proteins-of-candida-parapsilosis
#7
Justyna Karkowska-Kuleta, Dorota Zajac, Grazyna Bras, Oliwia Bochenska, Maria Rapala-Kozik, Andrzej Kozik
Pathogenic microbes can recruit to their cell surface human proteins that are components of important proteolytic cascades involved in coagulation, fibrinolysis and innate immune response. Once located at the bacterial or fungal surface, such deployed proteins might be utilized by pathogens to facilitate invasion and dissemination within the host organism by interfering with functionality of these systems or by exploiting specific activity of the bound enzymes. Aim of the study presented here was to characterize this phenomenon in Candida parapsilosis (Ashford) Langeron et Talice - an important causative agent of systemic fungal infections (candidiases and candidemias) in humans...
June 24, 2017: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/28651018/meta-analysis-of-mirna-expression-profiles-for-prostate-cancer-recurrence-following-radical-prostatectomy
#8
Elnaz Pashaei, Elham Pashaei, Maryam Ahmady, Mustafa Ozen, Nizamettin Aydin
BACKGROUND: Prostate cancer (PCa) is a leading reason of death in men and the most diagnosed malignancies in the western countries at the present time. After radical prostatectomy (RP), nearly 30% of men develop clinical recurrence with high serum prostate-specific antigen levels. An important challenge in PCa research is to identify effective predictors of tumor recurrence. The molecular alterations in microRNAs are associated with PCa initiation and progression. Several miRNA microarray studies have been conducted in recurrence PCa, but the results vary among different studies...
2017: PloS One
https://www.readbyqxmd.com/read/28651017/crystal-structure-of-middle-east-respiratory-syndrome-coronavirus-helicase
#9
Wei Hao, Justyna Aleksandra Wojdyla, Rong Zhao, Ruiyun Han, Rajat Das, Ivan Zlatev, Muthiah Manoharan, Meitian Wang, Sheng Cui
Middle East respiratory syndrome coronavirus (MERS-CoV) remains a threat to public health worldwide; however, effective vaccine or drug against CoVs remains unavailable. CoV helicase is one of the three evolutionary most conserved proteins in nidoviruses, thus making it an important target for drug development. We report here the first structure of full-length coronavirus helicase, MERS-CoV nsp13. MERS-CoV helicase has multiple domains, including an N-terminal Cys/His rich domain (CH) with three zinc atoms, a beta-barrel domain and a C-terminal SF1 helicase core with two RecA-like subdomains...
June 26, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28650998/functional-annotation-of-alzheimer-s-disease-associated-loci-revealed-by-gwass
#10
Zengpeng Han, Han Huang, Yue Gao, Qingyang Huang
Genome-wide association studies (GWASs) discovered a number of SNPs and genes associated with Alzheimer's disease (AD). However, how these SNPs and genes influence the liability to AD is not fully understood. We deployed computational approaches to explore the function and action mechanisms of AD -related SNPs and genes identified by GWASs, including the effects of 195 GWAS lead SNPs and 338 proxy SNPs on miRNAs binding and protein phosphorylation, their RegulomeDB and 3DSNP scores, and gene ontology, pathway enrichment and protein-protein interaction network of 126 AD-associated genes...
2017: PloS One
https://www.readbyqxmd.com/read/28650995/septins-restrict-inflammation-and-protect-zebrafish-larvae-from-shigella-infection
#11
Maria J Mazon-Moya, Alexandra R Willis, Vincenzo Torraca, Laurent Boucontet, Avinash R Shenoy, Emma Colucci-Guyon, Serge Mostowy
Shigella flexneri, a Gram-negative enteroinvasive pathogen, causes inflammatory destruction of the human colonic epithelium. Infection by S. flexneri has been well-studied in vitro and is a paradigm for bacterial interactions with the host immune system. Recent work has revealed that components of the cytoskeleton have important functions in innate immunity and inflammation control. Septins, highly conserved cytoskeletal proteins, have emerged as key players in innate immunity to bacterial infection, yet septin function in vivo is poorly understood...
June 26, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28650961/mfpred-rapid-and-accurate-prediction-of-protein-peptide-recognition-multispecificity-using-self-consistent-mean-field-theory
#12
Aliza B Rubenstein, Manasi A Pethe, Sagar D Khare
Multispecificity-the ability of a single receptor protein molecule to interact with multiple substrates-is a hallmark of molecular recognition at protein-protein and protein-peptide interfaces, including enzyme-substrate complexes. The ability to perform structure-based prediction of multispecificity would aid in the identification of novel enzyme substrates, protein interaction partners, and enable design of novel enzymes targeted towards alternative substrates. The relatively slow speed of current biophysical, structure-based methods limits their use for prediction and, especially, design of multispecificity...
June 26, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28650960/phosphatidylserine-externalization-necroptotic-bodies-release-and-phagocytosis-during-necroptosis
#13
Sefi Zargarian, Inbar Shlomovitz, Ziv Erlich, Aria Hourizadeh, Yifat Ofir-Birin, Ben A Croker, Neta Regev-Rudzki, Liat Edry-Botzer, Motti Gerlic
Necroptosis is a regulated, nonapoptotic form of cell death initiated by receptor-interacting protein kinase-3 (RIPK3) and mixed lineage kinase domain-like (MLKL) proteins. It is considered to be a form of regulated necrosis, and, by lacking the "find me" and "eat me" signals that are a feature of apoptosis, necroptosis is considered to be inflammatory. One such "eat me" signal observed during apoptosis is the exposure of phosphatidylserine (PS) on the outer plasma membrane. Here, we demonstrate that necroptotic cells also expose PS after phosphorylated mixed lineage kinase-like (pMLKL) translocation to the membrane...
June 26, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28650848/ser-thr-protein-kinase-b2-nadph-oxidase-2-signaling-in-thromboinflammation
#14
Jing Li, Jaehyung Cho
PURPOSE OF REVIEW: Interactions between neutrophils and platelets contribute to the progression of thromboinflammatory disease. However, the regulatory mechanism governing these interactions is poorly understood. The present review focuses on the crucial role of Ser/Thr protein kinase B (AKT)2-NADPH oxidase 2 (NOX2) signaling in regulating neutrophil and platelet activation and their heterotypic interactions under thromboinflammatory conditions. RECENT FINDINGS: Growing evidence has shown that platelets, leukocytes, and blood coagulation need to be considered to treat thromboinflammatory disease in which inflammation and thrombosis occur concurrently...
June 24, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28650821/detecting-essential-proteins-based-on-network-topology-gene-expression-data-and-gene-ontology-information
#15
Wei Zhang, Jia Xu, Yuanyuan Li, Xiufen Zou
The identification of essential proteins in protein-protein interaction (PPI) networks is of great significance for understanding cellular processes. With the increasing availability of large-scale PPI data, numerous centrality measures based on network topology have been proposed to detect essential proteins from PPI networks. However, most of the current approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology annotation information. In this paper, we propose a novel centrality measure, called TEO, for identifying essential proteins by combining network topology, gene expression profiles and GO information...
October 7, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28650797/larp1-functions-as-a-molecular-switch-for-mtorc1-mediated-translation-of-an-essential-class-of-mrnas
#16
Sungki Hong, Mallory A Freeberg, Ting Han, Avani Kamath, Yao Yao, Tomoko Fukuda, Tsukasa Suzuki, John K Kim, Ken Inoki
The RNA binding protein, LARP1, has been proposed to function downstream of mTORC1 to regulate the translation of 5'TOP mRNAs such as those encoding ribosome proteins (RP). However, the roles of LARP1 in the translation of 5'TOP mRNAs are controversial and its regulatory roles in mTORC1-mediated translation remain unclear. Here we show that LARP1 is a direct substrate of mTORC1 and Akt/S6K1. Deep sequencing of LARP1-bound mRNAs reveal that non-phosphorylated LARP1 interacts with both 5' and 3'UTRs of RP mRNAs and inhibits their translation...
June 26, 2017: ELife
https://www.readbyqxmd.com/read/28650657/noncovalent-pegylation-through-protein-polyelectrolyte-interaction-kinetic-experiment-and-molecular-dynamics-simulation
#17
Takaaki Kurinomaru, Kengo Kuwada, Shunsuke Tomita, Tomoshi Kameda, Kentaro Shiraki
Noncovalent binding of polyethylene glycol (PEG) to a protein surface is a unique protein handling technique to control protein function and stability. A diblock copolymer containing PEG and polyelectrolyte chains (PEGylated polyelectrolyte) is a promising candidate for noncovalent attachment of PEG to a protein surface because of the binding through multiple electrostatic interactions without protein denaturation. To obtain a deeper understanding of protein-polyelectrolyte interaction at the molecular level, we investigated the manner in which cationic PEGylated polyelectrolyte binds to anionic α-amylase in enzyme kinetic experiments and molecular dynamics (MD) simulations...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28650638/identification-and-structure-activity-relationships-of-novel-compounds-that-potentiate-the-activities-of-antibiotics-in-escherichia-coli
#18
Keith M Haynes, Narges Abdali, Varsha Jhawar, Helen I Zgurskaya, Jerry M Parks, Adam T Green, Jerome Yves Baudry, Valentin V Rybenkov, Jeremy C Smith, John K Walker
In Gram-negative bacteria, efflux pumps are able to prevent effective cellular concentrations from being achieved for a number of antibiotics. Small molecule adjuvants that act as efflux pump inhibitors (EPIs) have the potential to reinvigorate existing antibiotics that are currently ineffective due to efflux mechanisms. Through a combination of rigorous experimental screening and in silico virtual screening we recently identified novel classes of EPIs that interact with the membrane fusion protein AcrA, a critical component of the AcrAB-TolC efflux pump in E...
June 26, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28650487/engineering-thiophene-based-nanoparticles-to-induce-phototransduction-in-live-cells-under-illumination
#19
M Zangoli, F Di Maria, E Zucchetti, C Bossio, M R Antognazza, G Lanzani, R Mazzaro, F Corticelli, M Baroncini, G Barbarella
We report that nanoparticles prepared from appropriately functionalized polythiophenes once administered to live cells can acquire phototransduction properties under illumination, becoming photoactive sites able to absorb visible light and convert it to an electrical signal through cell membrane polarization. Amine-reactive fluorescent nanoparticles with pendant N-succinimidyl-ester groups (NPs-NHS) are prepared from polythiophenes alternating unsubstituted and 3-(2,5-dioxopyrrolidin-1-yl-8-octanoate)-substituted thiophenes by a nanoprecipitation method...
June 26, 2017: Nanoscale
https://www.readbyqxmd.com/read/28650476/cry2h-seq-a-massively-multiplexed-assay-for-deep-coverage-interactome-mapping
#20
Shelly A Trigg, Renee M Garza, Andrew MacWilliams, Joseph R Nery, Anna Bartlett, Rosa Castanon, Adeline Goubil, Joseph Feeney, Ronan O'Malley, Shao-Shan C Huang, Zhuzhu Z Zhang, Mary Galli, Joseph R Ecker
Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. Here, we present a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse. We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions...
June 26, 2017: Nature Methods
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