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https://www.readbyqxmd.com/read/27914082/detection-of-intracellular-proteins-by-high-resolution-immunofluorescence-microscopy-in-streptococcus-pyogenes
#1
Assaf Raz
Immunofluorescence microscopy is an invaluable tool for the study of biological processes at the cellular level. While the localization of surface-exposed antigens can easily be determined using fluorescent antibodies, localization of intracellular antigens requires permeabilization of the bacterial cell wall and membrane. Here, we describe an immunofluorescence protocol tailored specifically for Streptococcus pyogenes, applying the phage lysin PlyC for cell wall permeabilization. This protocol allows a high level of morphological preservation, suitable for high-resolution microscopy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#2
Christine E Tinberg, Sagar D Khare
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914060/a-protocol-for-the-design-of-protein-and-peptide-nanostructure-self-assemblies-exploiting-synthetic-amino-acids
#3
Nurit Haspel, Jie Zheng, Carlos Aleman, David Zanuy, Ruth Nussinov
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914048/geometric-potentials-for-computational-protein-sequence-design
#4
Jie Li, Patrice Koehl
Computational protein sequence design is the rational design based on computer simulation of new protein molecules to fold to target three-dimensional structures, with the ultimate goal of designing novel functions. It requires a good understanding of the thermodynamic equilibrium properties of the protein of interest. Here, we consider the contribution of the solvent to the stability of the protein. We describe implicit solvent models, focusing on approximations of their nonpolar components using geometric potentials...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914010/recruitment-by-the-repressor-freud-1-of-histone-deacetylase-brg1-chromatin-remodeling-complexes-to-strengthen-htr1a-gene-repression
#5
Tatiana Souslova, Kim Mirédin, Anne M Millar, Paul R Albert
Five-prime repressor element under dual repression binding protein-1 (Freud-1)/CC2D1A is genetically linked to intellectual disability and implicated in neuronal development. Freud-1 represses the serotonin-1A (5-HT1A) receptor gene HTR1A by histone deacetylase (HDAC)-dependent or HDAC-independent mechanisms in 5-HT1A-negative (e.g., HEK-293) or 5-HT1A-expressing cells (SK-N-SH), respectively. To identify the underlying mechanisms, Freud-1-associated proteins were affinity-purified from HEK-293 nuclear extracts and members of the Brg1/SMARCCA chromatin remodeling and Sin3A-HDAC corepressor complexes were identified...
December 2, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27914009/serum-response-factor-srf-ablation-interferes-with-acute-stress-associated-immediate-and-long-term-coping-mechanisms
#6
Annemarie Zimprich, Gabi Mroz, Christopher Meyer Zu Reckendorf, Sofia Anastasiadou, Philip Förstner, Lillian Garrett, Sabine M Hölter, Lore Becker, Jan Rozman, Cornelia Prehn, Birgit Rathkolb, Kristin Moreth, Wolfgang Wurst, Thomas Klopstock, Martin Klingenspor, Jerzy Adamski, Eckhard Wolf, Raffi Bekeredjian, Helmut Fuchs, Valerie Gailus-Durner, Martin Hrabe de Angelis, Bernd Knöll
Stress experience modulates behavior, metabolism, and energy expenditure of organisms. One molecular hallmark of an acute stress response is a rapid induction of immediate early genes (IEGs) such as c-Fos and Egr family members. IEG transcription in neurons is mediated by the neuronal activity-driven gene regulator serum response factor (SRF). We show a first role of SRF in immediate and long-lasting acute restraint stress (AS) responses. For this, we employed a standardized mouse phenotyping protocol at the German Mouse Clinic (GMC) including behavioral, metabolic, and cardiologic tests as well as gene expression profiling to analyze the consequences of forebrain-specific SRF deletion in mice exposed to AS...
December 2, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27914002/phenotypic-and-genotypic-characterization-of-bacteriocinogenic-enterococci-against-clostridium-botulinum
#7
Awad A Shehata, Reda Tarabees, Shereen Basiouni, Mahmoud Gamil, Ahmed S Kamal, Monika Krüger
The present study aimed to characterize Enterococcus faecalis (n = -6) and Enterococcus faecium (n = 1) isolated from healthy chickens to find a novel perspective probiotic candidate that antagonize Clostridium botulinum types A, B, D, and E. The isolated enterococci were characterized based on phenotypic properties, PCR, and matrix-assisted laser desorption/ionization time of flight (MALDI-TOF). The virulence determinants including hemolytic activity on blood agar, gelatinase activity, sensitivity to vancomycin, and presence of gelatinase (gelE) and enterococcal surface protein (esp) virulence genes were investigated...
December 2, 2016: Probiotics and Antimicrobial Proteins
https://www.readbyqxmd.com/read/27913905/proteins-immunologically-related-to-map65-1-accumulate-and-localize-differentially-during-bud-development-in-vitis-vinifera-l
#8
Luigi Parrotta, Claudia Faleri, Mauro Cresti, Giampiero Cai
Various arrays of microtubules are present throughout the plant cell cycle and are involved in distinct functions. Microtubule-associated proteins (MAPs) regulate microtubule dynamics by acting as stabilizers, destabilizers, and promoters of microtubule dynamics. The MAP65 family is a specific group of cross-linkers required for structural maintenance of microtubules. In plants, different isoforms of MAP65 are differentially expressed according to their developmental program. In this work, we analyzed the differential distribution of proteins immunologically related to MAP65-1 during bud development in grapevine (Vitis vinifera L...
December 2, 2016: Protoplasma
https://www.readbyqxmd.com/read/27913822/more-than-just-scanning-the-importance-of-cap-independent-mrna-translation-initiation-for-cellular-stress-response-and-cancer
#9
REVIEW
Rafaela Lacerda, Juliane Menezes, Luísa Romão
The scanning model for eukaryotic mRNA translation initiation states that the small ribosomal subunit, along with initiation factors, binds at the cap structure at the 5' end of the mRNA and scans the 5' untranslated region (5'UTR) until an initiation codon is found. However, under conditions that impair canonical cap-dependent translation, the synthesis of some proteins is kept by alternative mechanisms that are required for cell survival and stress recovery. Alternative modes of translation initiation include cap- and/or scanning-independent mechanisms of ribosomal recruitment...
December 2, 2016: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/27913762/aspen-felanpe-clinical-guidelines-nutrition-support-of-adult-patients-with-enterocutaneous-fistula
#10
Vanessa J Kumpf, Jose Eduardo de Aguilar-Nascimento, Jose Ignacio Diaz-Pizarro Graf, Amber M Hall, Liam McKeever, Ezra Steiger, Marion F Winkler, Charlene W Compher
BACKGROUND: The management of patients with enterocutaneous fistula (ECF) requires an interdisciplinary approach and poses a significant challenge to physicians, wound/stoma care specialists, dietitians, pharmacists, and other nutrition clinicians. Guidelines for optimizing nutrition status in these patients are often vague, based on limited and dated clinical studies, and typically rely on individual institutional or clinician experience. Specific nutrient requirements, appropriate route of feeding, role of immune-enhancing formulas, and use of somatostatin analogues in the management of patients with ECF are not well defined...
December 2, 2016: JPEN. Journal of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/27913740/a-%C3%AE-ketoacyl-coa-synthase-is-involved-in-rice-leaf-cuticular-wax-synthesis-and-requires-a-cer2-like-protein-as-a-cofactor
#11
Xiaochen Wang, Yuanyuan Guan, Du Zhang, Xiangbai Dong, Lihong Tian, Le Qing Qu
Cuticular waxes are complex mixtures of very-long-chain fatty acids (VLCFAs) and their derivatives, forming a natural barrier on aerial surfaces of terrestrial plants against biotic and abiotic stresses. In VLCFA biosynthesis, β-ketoacyl-CoA synthase (KCS) is the key enzyme, catalyzing the first reaction in fatty acid elongation and determining substrate specificity. We isolated a rice (Oryza sativa L.) wax crystal-sparse leaf 4 (WSL4) gene using a map-based cloning strategy. WSL4 is predicted to encode a KCS, a homolog of Arabidopsis CER6...
December 2, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27913673/structural-insights-into-functional-amyloid-inhibition-in-gram-ve-bacteria
#12
REVIEW
William Hawthorne, Sarah Rouse, Lee Sewell, Stephen J Matthews
Amyloids are proteinaceous aggregates known for their role in debilitating degenerative diseases involving protein dysfunction. Many forms of functional amyloid are also produced in nature and often these systems require careful control of their assembly to avoid the potentially toxic effects. The best-characterised functional amyloid system is the bacterial curli system. Three natural inhibitors of bacterial curli amyloid have been identified and recently characterised structurally. Here, we compare common structural features of CsgC, CsgE and CsgH and discuss the potential implications for general inhibition of amyloid...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913654/novel-small-molecule-jp-153-targets-the-src-fak-paxillin-signaling-complex-to-inhibit-vegf-induced-retinal-angiogenesis
#13
Jordan J Toutounchian, Jayaprakash Pagadala, Duane D Miller, Jerome Baudry, Frank Park, Edward Chaum, Charles R Yates
Targeting vascular endothelial growth factor (VEGF) is a common treatment strategy for neovascular eye disease, a major cause of vision loss in diabetic retinopathy and age-related macular degeneration. However, the decline in clinical efficacy over time in many patients suggests that monotherapy of anti-VEGF protein therapeutics may benefit from adjunctive treatments. Our previous work has shown that through decreased activation of the cytoskeletal protein paxillin, growth factor-induced ischemic retinopathy in the murine oxygen-induced retinopathy model could be inhibited...
January 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/27913624/bcp1-is-the-nuclear-chaperone-of-the-60s-ribosomal-protein-rpl23-in-saccharomyces-cerevisiae
#14
Ya-Han Ting, Ting-Jun Lu, Arlen W Johnson, Jing-Ting Shie, Bo-Ru Chen, Suresh Kumar S, Kai-Yin Lo
Eukaryotic ribosomes are composed of rRNAs and ribosomal proteins. Ribosomal proteins are translated in the cytoplasm and imported into the nucleus for assembly with the rRNAs. It has been shown that chaperones or karyopherins responsible for import can maintain the stability of ribosomal proteins by neutralizing unfavorable positive charges and thus facilitate their transports. Among 79 ribosomal proteins in yeast, only few are identified with specific chaperones. Besides the classic role in maintaining protein stability, chaperones have additional roles in transport, chaperoning the assembly site, and dissociation of ribosomal proteins from karyopherins...
December 2, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27913618/meiotic-centromere-coupling-and-pairing-function-by-two-separate-mechanisms-in-saccharomyces-cerevisiae
#15
Emily L Kurdzo, David Obeso, Hoa Chuong, Dean S Dawson
In meiosis I, chromosomes become paired with their homologous partners and then are pulled towards opposite poles of the spindle. In the budding yeast, Saccharomyces cerevisiae, in early meiotic prophase, centromeres are observed to associate in pairs in a homology-independent manner, a process called centromere coupling. Later, as homologous chromosomes align, their centromeres associate in a process called centromere pairing. The synaptonemal complex protein Zip1 is necessary for both types of centromere association...
December 2, 2016: Genetics
https://www.readbyqxmd.com/read/27913545/what-have-we-learned-from-large-population-studies-of-von-willebrand-disease
#16
Robert R Montgomery, Veronica H Flood
Von Willebrand factor (VWF) is a critical regulator of hemostatic processes, including collagen binding, platelet adhesion, and platelet aggregation. It also serves as a carrier protein to normalize plasma factor VIII synthesis, release, and survival. While VWF protein measurements by immunoassay are reasonably comparable between institutions, the measurement of VWF ristocetin cofactor activity (VWF:RCo) has significant variability. Other tests of VWF function, including collagen binding or platelet glycoprotein IIb-IIIa binding, are not universally available, yet these functional defects may cause major bleeding even with normal VWF antigen (VWF:Ag) and VWF:RCo assays...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27913309/sequence-determinants-of-the-caenhorhabditis-elegansdopamine-transporter-dictating-in-vivoaxonal-export-and-synaptic-localization
#17
Sarah B Robinson, J Andrew Hardaway, Shannon L Hardie, Jane Wright, Ryan M Glynn, Daniel P Bermingham, Qiao Han, Sarah M Sturgeon, Phyllis Freeman, Randy D Blakely
The monoamine neurotransmitter dopamine (DA) acts across phylogeny to modulate both simple and complex behaviors. The presynaptic DA transporter (DAT) is a major determinant of DA signaling capacity in ensuring efficient extracellular DA clearance. In humans, DAT is also a major target for prescribed and abused psychostimulants. Multiple structural determinants of DAT function and regulation have been defined, though largely these findings have arisen from heterologous expression or ex vivo cell culture studies...
November 29, 2016: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/27913308/biodegradable-magnetic-silica-iron-oxide-nanovectors-with-ultra-large-mesopores-for-high-protein-loading-magnetothermal-release-and-delivery
#18
Haneen Omar, Jonas G Croissant, Kholod Alamoudi, Shahad Alsaiari, Ibrahim Alradwan, Majed A Majrashi, Dalaver H Anjum, Patricia Martins, Basem Moosa, Abdulaziz Almalik, Niveen M Khashab
The delivery of large cargos of diameter above 15nm for biomedical applications has proved challenging since it requires biocompatible, stably-loaded, and biodegradable nanomaterials. In this study, we describe the design of biodegradable silica-iron oxide hybrid nanovectors with large mesopores for large protein delivery in cancer cells. The mesopores of the nanomaterials spanned from 20 to 60nm in diameter and post-functionalization allowed the electrostatic immobilization of large proteins (e.g. mTFP-Ferritin, ~534kDa)...
November 29, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/27913296/regulation-of-skeletal-muscle-insulin-stimulated-signaling-through-the-mek-redd1-mtor-axis
#19
Cory M Dungan, David L Williamson
Recent findings in adipocytes suggest that mitogen-activated protein kinase (MAPK)/extracellular-regulated signaling kinase (ERK) kinase 1/2 (MEK1/2) signaling regulates regulated in development and DNA damage 1 (REDD1) protein expression. Similarly, our previous work show that a lack of REDD1 protein expression, and associated hyperactive basal mechanistic target of rapamycin (mTOR) signaling, limits skeletal muscle's response to insulin. Therefore, we sought to determine: 1) if MEK1/2 inhibition is sufficient to reduce REDD1 protein expression and subsequently insulin receptor substrate-1 (IRS-1) tyrosine phosphorylation via negative feedback of hyperactive mTOR in REDD1 wild-type (WT) mice and 2) if rapamycin-mediated mTOR inhibition is sufficient to improve IRS-1 tyrosine phosphorylation in REDD1 knockout (KO) mice...
November 29, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27913293/differential-role-of-calpain-dependent-protein-cleavage-in-intermediate-and-long-term-operant-memory-in-aplysia
#20
Lisa C Lyons, Jacob S Gardner, Cassidy T Lentsch, Catherine E Gandour, Harini C Krishnan, Eric J Noakes
In addition to protein synthesis, protein degradation or protein cleavage may be necessary for intermediate (ITM) and long-term memory (LTM) to remove molecular constraints, facilitate persistent kinase activity and modulate synaptic plasticity. Calpains, a family of conserved calcium dependent cysteine proteases, modulate synaptic function through protein cleavage. We used the marine mollusk Aplysia californica to investigate the in vivo role of calpains during intermediate and long-term operant memory formation using the learning that food is inedible (LFI) paradigm...
November 29, 2016: Neurobiology of Learning and Memory
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