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https://www.readbyqxmd.com/read/27914069/protein-based-strategies-to-identify-and-isolate-bacterial-virulence-factors
#1
Rolf Lood, Inga-Maria Frick
Protein-protein interactions play important roles in bacterial pathogenesis. Surface-bound or secreted bacterial proteins are key in mediating bacterial virulence. Thus, these factors are of high importance to study in order to elucidate the molecular mechanisms behind bacterial pathogenesis. Here, we present a protein-based strategy that can be used to identify and isolate bacterial proteins of importance for bacterial virulence, and allow for identification of both unknown host and bacterial factors. The methods described have among others successfully been used to identify and characterize several IgG-binding proteins, including protein G, protein H, and protein L...
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/27914050/multistate-computational-protein-design-with-backbone-ensembles
#3
James A Davey, Roberto A Chica
The ability of computational protein design (CPD) to identify protein sequences possessing desired characteristics in vast sequence spaces makes it a highly valuable tool in the protein engineering toolbox. CPD calculations are typically performed using a single-state design (SSD) approach in which amino-acid sequences are optimized on a single protein structure. Although SSD has been successfully applied to the design of numerous protein functions and folds, the approach can lead to the incorrect rejection of desirable sequences because of the combined use of a fixed protein backbone template and a set of rigid rotamers...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914037/expression-of-mrna-and-protein-of-il-18-and-its-receptor-in-human-follicular-granulosa-cells
#4
A Salmassi, A Fattahi, M Nouri, J Hedderich, A G Schmutzler
PURPOSE: There is no information available about the IL-18 receptor in ovarian follicles, so the present study attempts to demonstrate the expression of IL-18 and its receptor in human granulosa cells (GCs). METHODS: To evaluate the concentration of IL-18 in serum and follicular fluid (FF), we collected serum and FF from 102 women undergoing oocyte retrieval. Also, to detect expression of IL-18 and its receptor by luteinized GCs, these cells were pooled six times from a total of twenty individual patients with 5-16 follicles each...
December 2, 2016: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/27914030/active-compounds-extracted-from-extra-virgin-olive-oil-counteract-mesothelial-to-mesenchymal-transition-of-peritoneal-mesothelium-cells-exposed-to-conventional-peritoneal-dialysate-in-vitro-and-in-vivo-evidences
#5
S Lupinacci, G Toteda, D Vizza, A Perri, C Benincasa, A Mollica, A La Russa, P Gigliotti, F Leone, D Lofaro, M Bonofiglio, E Perri, R Bonofiglio
During peritoneal dialysis (PD), peritoneal mesothelial cells undergo a transition from an epithelial phenotype to a mesenchymal phenotype that, together with the inflammatory process, promotes tissue fibrosis and a failure of peritoneal membrane function. To date, there is no definitive treatment for the progressive thickening and angiogenesis of the peritoneal membrane associated with PD. In this study we tested, in vitro and in vivo, the ability of active compounds extracted from extra virgin olive oil (AC-EVOO) to counteract the mesothelial-to-mesenchymal transition process (MMT) observed in mesothelial cells chronically exposed to the conventional peritoneal dialysate (DL)...
December 2, 2016: Journal of Nephrology
https://www.readbyqxmd.com/read/27914010/recruitment-by-the-repressor-freud-1-of-histone-deacetylase-brg1-chromatin-remodeling-complexes-to-strengthen-htr1a-gene-repression
#6
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/27914001/subtilosin-prevents-biofilm-formation-by-inhibiting-bacterial-quorum-sensing
#7
Ammar Algburi, Saskia Zehm, Victoria Netrebov, Anzhelica B Bren, Vladimir Chistyakov, Michael L Chikindas
Subtilosin, the cyclic lantibiotic protein produced by Bacillus subtilis KATMIRA1933, targets the surface receptor and electrostatically binds to the bacterial cell membrane. In this study, subtilosin was purified using ammonium sulfate ((NH4)2SO4) precipitation and purified via column chromatography. Subtilosin's antibacterial minimum and sub-minimum inhibitory concentrations (MIC and sub-MIC) and anti-biofilm activity (biofilm prevention) were established. Subtilosin was evaluated as a quorum sensing (QS) inhibitor in Gram-positive bacteria using Fe(III) reduction assay...
December 2, 2016: Probiotics and Antimicrobial Proteins
https://www.readbyqxmd.com/read/27913948/branched-chain-amino-acids-administration-suppresses-endurance-exercise-related-activation-of-ubiquitin-proteasome-signaling-in-trained-human-skeletal-muscle
#8
Evgeny A Lysenko, Tatiana F Vepkhvadze, Egor M Lednev, Olga L Vinogradova, Daniil V Popov
We tested whether post exercise ingestion of branched-chain amino acids (BCAA < 10 g) is sufficient to activate signaling associated with muscle protein synthesis and suppress exercise-induced activation of mechanisms associated with proteolysis in endurance-trained human skeletal muscle. Nine endurance-trained athletes performed a cycling bout with and without BCAA ingestion (0.1 g/kg). Post exercise ACC(Ser79/222) phosphorylation (endogenous marker of AMPK activity) was increased (~3-fold, P < 0...
December 3, 2016: Journal of Physiological Sciences: JPS
https://www.readbyqxmd.com/read/27913854/the-role-of-macromolecules-in-the-formation-of-kidney-stones
#9
REVIEW
Jeffrey D Rimer, Ann M Kolbach-Mandel, Michael D Ward, Jeffrey A Wesson
The formation of crystal aggregates, one of the critical processes in kidney stone pathogenesis, involves interactions between crystals (predominantly calcium oxalate monohydrate, COM) and urinary constituents (e.g., proteins), which serve as an adhesive "glue" between crystals in stones. To develop a better understanding of the protein-crystal interactions that lead to crystal aggregation, we have measured the effect of model proteins on bulk COM crystal properties as well as their adsorption on crystal surfaces using three synthetic polyanions: poly(aspartic acid) (polyD), poly(glutamic acid) (polyE), and poly(acrylic acid) (polyAA)...
December 2, 2016: Urolithiasis
https://www.readbyqxmd.com/read/27913845/mitogen-activated-protein-kinases-are-involved-in-hepatocanalicular-dysfunction-and-cholestasis-induced-by-oxidative-stress
#10
Flavia D Toledo, Cecilia L Basiglio, Ismael R Barosso, Andrea C Boaglio, Andrés E Zucchetti, Enrique J Sánchez Pozzi, Marcelo G Roma
In previous studies, we showed that the pro-oxidant model agent tert-butyl hydroperoxide (tBuOOH) induces alterations in hepatocanalicular secretory function by activating Ca(2+)-dependent protein kinase C isoforms (cPKC), via F-actin disorganization followed by endocytic internalization of canalicular transporters relevant to bile formation (Mrp2, Bsep). Since mitogen-activated protein kinases (MAPKs) may be downstream effectors of cPKC, we investigated here the involvement of the MAPKs of the ERK1/2, JNK1/2, and p38(MAPK) types in these deleterious effects...
December 2, 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/27913728/fission-yeast-stn1-is-crucial-for-semi-conservative-replication-at-telomeres-and-subtelomeres
#11
Masahiro Takikawa, Yusuke Tarumoto, Fuyuki Ishikawa
The CST complex is a phylogenetically conserved protein complex consisting of CTC1/Cdc13, Stn1 and Ten1 that protects telomeres on linear chromosomes. Deletion of the fission yeast homologs stn1 and ten1 results in complete telomere loss; however, the precise function of Stn1 is still largely unknown. Here, we have isolated a high-temperature sensitive stn1 allele (termed stn1-1). stn1-1 cells abruptly lost telomeric sequence almost completely at the restrictive temperature. The loss of chromosomal DNA happened without gradual telomere shortening, and extended to 30 kb from the ends of chromosomes...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913688/left-ventricle-transcriptomic-analysis-reveals-connective-tissue-accumulation-associates-with-initial-age-dependent-decline-in-v%C3%AC-o2peak-from-its-lifetime-apex
#12
Gregory N Ruegsegger, Ryan G Toedebusch, Joshua F Braselton, Thomas E Childs, Frank W Booth
Peak oxygen consumption (V̇O2peak) strongly predicts morbidity and mortality better than other established risk factors, yet mechanisms associated with its age-associated decline are unknown. Our lab has shown that V̇O2peak first begins to decrease at the same age of 19-20 weeks old in both sedentary and wheel-running, female Wistar rats (Toedebusch et al., Physiol Genomics. 48:101-15, 2016). Here, we employed a total systemic approach using unsupervised interrogation of mRNA with RNA-sequencing. The purpose of our study was to analyze transcriptomic profiles from both sedentary (SED) and wheel-running (RUN) conditions as a strategy to identify pathways in the left ventricle that may contribute to the initial reductions in V̇O2peak occurring between 19 and 27 weeks of age...
December 2, 2016: Physiological Genomics
https://www.readbyqxmd.com/read/27913687/do-we-know-whether-potential-g-quadruplexes-actually-form-in-long-functional-rna-molecules
#13
REVIEW
Carika Weldon, Ian C Eperon, Cyril Dominguez
The roles of deoxyribonucleic acid (DNA) G-quadruplex structures in gene expression and telomere maintenance have been well characterized. Recent results suggest that such structures could also play pivotal roles in ribonucleic acid (RNA) biology, such as splicing or translation regulation. However, it has been difficult to show that RNA G-quadruplexes (G4s) exist in specific long RNA sequences, such as precursor messenger RNA, in a functional or cellular context. Most current methods for identifying G4s involve the use of short, purified RNA sequences in vitro, in the absence of competition with secondary structures or protein binding...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913672/first-model-of-dimeric-lrrk2-the-challenge-of-unrevealing-the-structure-of-a-multidomain-parkinson-s-associated-protein
#14
REVIEW
Giambattista Guaitoli, Bernd K Gilsbach, Francesco Raimondi, Christian Johannes Gloeckner
Mutations within the leucine-rich repeat kinase 2 (LRRK2) gene represent the most common cause of Mendelian forms of Parkinson's disease, among autosomal dominant cases. Its gene product, LRRK2, is a large multidomain protein that belongs to the Roco protein family exhibiting GTPase and kinase activity, with the latter activity increased by pathogenic mutations. To allow rational drug design against LRRK2 and to understand the cross-regulation of the G- and the kinase domain at a molecular level, it is key to solve the three-dimensional structure of the protein...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913669/the-unconventional-g-protein-cycle-of-lrrk2-and-roco-proteins
#15
REVIEW
Susanne Terheyden, Laura M Nederveen-Schippers, Arjan Kortholt
Mutations in the human leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of hereditary Parkinson's disease (PD). LRRK2 belongs to the Roco family of proteins, which are characterized by the presence of a Ras of complex proteins domain (Roc), a C-terminal of Roc domain (COR) and a kinase domain. Despite intensive research, much remains unknown about activity and the effect of PD-associated mutations. Recent biochemical and structural studies suggest that LRRK2 and Roco proteins are noncanonical G-proteins that do not depend on guanine nucleotide exchange factors or GTPase-activating proteins for activation...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913664/receptor-activity-modifying-protein-directed-g-protein-signaling-specificity-for-the-calcitonin-gene-related-peptide-family-of-receptors
#16
Cathryn Weston, Ian Winfield, Matthew Harris, Rose Hodgson, Archna Shah, Simon J Dowell, Juan Carlos Mobarec, David A Woodcock, Christopher A Reynolds, David R Poyner, Harriet A Watkins, Graham Ladds
No abstract text is available yet for this article.
December 2, 2016: Journal of Biological Chemistry
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/27913282/proteomics-provides-insights-into-biological-pathways-altered-by-plant-growth-promoting-bacteria-and-arbuscular-mycorrhiza-in-sorghum-grown-in-marginal-soil
#19
Faten Dhawi, Rupali Datta, Wusirika Ramakrishna
Sorghum is an economically important crop, a model system for gene discovery and a biofuel source. Sorghum seedlings were subjected to three microbial treatments, plant growth promoting bacteria (B), arbuscular mycorrhizal (AM) fungi mix with two Glomus species (G. aggregatum and G. etunicatum), Funelliformis mosseae and Rhizophagus irregularis (My), and B and My combined (My+B). Proteomic analysis was conducted followed by integration with metabolite, plant biomass and nutrient data. Out of 366 differentially expressed proteins in sorghum roots, 44 upregulated proteins overlapping among three treatment groups showed positive correlation with sorghum biomass or element uptake or both...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27913276/association-of-genetic-polymorphisms-of-angiopoietin-like-4-with-severity-of-posttransplant-proteinuria-in-kidney-allograft-recipients
#20
Youngil Chang, Tariq Shah, Jaewook Yang, David I Min
BACKGROUND: Proteinuria is a hallmark of glomerular injury, and persistent proteinuria is associated with graft failure in kidney transplant patients. Recently, it is known that the level of circulating angiopoietin-like 4 (ANGPTL4) is elevated in the patients with human nephrotic syndrome, in which ANGPTL4 is responsible for relieving proteinuria. PURPOSE: The purpose of this study is to determine effects of clinical factors and genetic polymorphism of ANGPTL4 on proteinuria after kidney transplantation...
November 29, 2016: Transplant Immunology
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