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https://www.readbyqxmd.com/read/29036679/human-recombinant-fab-fragment-from-combinatorial-libraries-of-a-b-cell-lymphoma-patient-recognizes-core-protein-of-chondroitin-sulfate-proteoglycan-4
#1
Yoko Egami, Yuta Narushima, Motohiro Ohshima, Akira Yoshida, Naruki Yoneta, Yasufumi Masaki, Kunihiko Itoh
CD antigens are well known as therapeutic targets of B-cell lymphoma. To isolate therapeutic antibodies that recognize novel targets other than CD antigens, we constructed a phage display combinatorial antibody Fab library from bone marrow lymphocytes of B-cell lymphoma patient. To eliminate antibodies reactive with known B-cell lymphoma antigen, non-hematopoietic and patient's sera reactive HeLaS3 cells was selected as a target of whole cell panning. Five rounds of panning against live HeLaS3 cells retrieved single Fab clone, termed AHSA (Antibody to HeLa Surface Antigen)...
September 28, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29036616/deeploc-prediction-of-protein-subcellular-localization-using-deep-learning
#2
José Juan Almagro Armenteros, Casper Kaae Sønderby, Søren Kaae Sønderby, Henrik Nielsen, Ole Winther
Motivation: The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036376/the-mechanism-and-high-free-energy-transition-state-of-lac-repressor-lac-operator-interaction
#3
Rituparna Sengupta, Michael W Capp, Irina A Shkel, M Thomas Record
Significant, otherwise-unavailable information about mechanisms and transition states (TS) of protein folding and binding is obtained from solute effects on rate constants. Here we characterize TS for lac repressor(R)-lac operator(O) binding by analyzing effects of RO-stabilizing and RO-destabilizing solutes on association (ka) and dissociation (kd) rate constants. RO-destabilizing solutes (urea, KCl) reduce ka comparably (urea) or more than (KCl) they increase kd, demonstrating that they destabilize TS relative to reactants and RO, and that TS exhibits most of the Coulombic interactions between R and O...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29035974/altered-ultrasonic-vocalization-in-neonatal-sapap3-deficient-mice
#4
Natalya S Tesdahl, Danielle K King, Latisha N McDaniel, Andrew A Pieper
Ultrasonic vocalizations (USVs) in neonatal mice provide a means of modeling communication deficits in neurodevelopmental disorders. Mature mice deficient in SAP90/PSD95-associated protein 3 (SAPAP3) display compulsive grooming and anxiety-like behavior, conditions that are often associated with neurodevelopmental disorders. To date, however, aspects of neurodevelopment have not been investigated in SAPAP3-deficient mice. Here, we examined whether neonatal SAPAP3-deficient mice display altered USVs. We recorded USVs from 5-day-old sapap3 and sapap3 mice, and also monitored developmental reflexes in these mice during the early postnatal period...
October 13, 2017: Neuroreport
https://www.readbyqxmd.com/read/29035839/insights-into-protein-misfolding-and-aggregation-enabled-by-solid-state-nmr-spectroscopy
#5
REVIEW
Patrick C A van der Wel
The aggregation of proteins and peptides into a variety of insoluble, and often non-native, aggregated states plays a central role in many devastating diseases. Analogous processes undermine the efficacy of polypeptide-based biological pharmaceuticals, but are also being leveraged in the design of biologically inspired self-assembling materials. This Trends article surveys the essential contributions made by recent solid-state NMR (ssNMR) studies to our understanding of the structural features of polypeptide aggregates, and how such findings are informing our thinking about the molecular mechanisms of misfolding and aggregation...
October 4, 2017: Solid State Nuclear Magnetic Resonance
https://www.readbyqxmd.com/read/29035537/discovery-of-a-novel-piperidine-based-inhibitor-of-cholesteryl-ester-transfer-protein-cetp-that-retains-activity-in-hypertriglyceridemic-plasma
#6
Ken Yamada, Margaret Brousseau, Wataru Honma, Akiko Iimura, Hidetomo Imase, Yuki Iwaki, Toshio Kawanami, Daniel LaSala, Guiqing Liang, Hironobu Mitani, Kazuhiko Nonomura, Osamu Ohmori, Meihui Pan, Dean F Rigel, Ichiro Umemura, Kayo Yasoshima, Guoming Zhu, Muneto Mogi
Herein we describe the discovery and characterization of a novel, piperidine-based inhibitor of cholesteryl ester transfer protein (CETP) with a core structure distinct from other reported CETP inhibitors. A versatile synthesis starting from 4-methoxypyridine enabled an efficient exploration of the SAR, giving a lead molecule with potent CETP inhibition in human plasma. The subsequent optimization focused on improvement of pharmacokinetics and mitigation of off-target liabilities, such as CYP inhibition, whose improvement correlated with increased lipophilic efficiency...
October 16, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29035306/platelet-endothelial-cell-adhesion-molecule-1-and-oligodendrogenesis-significance-in-alcohol-use-disorders
#7
REVIEW
Chitra D Mandyam, Emmanuel G Villalpando, Noah L Steiner, Leon W Quach, McKenzie J Fannon, Sucharita S Somkuwar
Alcoholism is a chronic relapsing disorder with few therapeutic strategies that address the core pathophysiology. Brain tissue loss and oxidative damage are key components of alcoholism, such that reversal of these phenomena may help break the addictive cycle in alcohol use disorder (AUD). The current review focuses on platelet endothelial cell adhesion molecule 1 (PECAM-1), a key modulator of the cerebral endothelial integrity and neuroinflammation, and a targetable transmembrane protein whose interaction within AUD has not been well explored...
October 16, 2017: Brain Sciences
https://www.readbyqxmd.com/read/29034217/evolution-of-salmonella-host-cell-interactions-through-a-dynamic-bacterial-genome
#8
REVIEW
Bushra Ilyas, Caressa N Tsai, Brian K Coombes
Salmonella Typhimurium has a broad arsenal of genes that are tightly regulated and coordinated to facilitate adaptation to the various host environments it colonizes. The genome of Salmonella Typhimurium has undergone multiple gene acquisition events and has accrued changes in non-coding DNA that have undergone selection by regulatory evolution. Together, at least 17 horizontally acquired pathogenicity islands (SPIs), prophage-associated genes, and changes in core genome regulation contribute to the virulence program of Salmonella...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29033332/disruption-of-core-planar-cell-polarity-signaling-regulates-renal-tubule-morphogenesis-but-is-not-cystogenic
#9
Koshi Kunimoto, Roy D Bayly, Eszter K Vladar, Tyson Vonderfecht, Anna-Rachel Gallagher, Jeffrey D Axelrod
Oriented cell division (OCD) and convergent extension (CE) shape developing renal tubules, and their disruption has been associated with polycystic kidney disease (PKD) genes, the majority of which encode proteins that localize to primary cilia. Core planar cell polarity (PCP) signaling controls OCD and CE in other contexts, leading to the hypothesis that disruption of PCP signaling interferes with CE and/or OCD to produce PKD. Nonetheless, the contribution of PCP to tubulogenesis and cystogenesis is uncertain, and two major questions remain unanswered...
October 11, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29033324/the-elongation-factor-spt6-maintains-esc-pluripotency-by-controlling-super-enhancers-and-counteracting-polycomb-proteins
#10
A Hongjun Wang, Aster H Juan, Kyung Dae Ko, Pei-Fang Tsai, Hossein Zare, Stefania Dell'Orso, Vittorio Sartorelli
Spt6 coordinates nucleosome dis- and re-assembly, transcriptional elongation, and mRNA processing. Here, we report that depleting Spt6 in embryonic stem cells (ESCs) reduced expression of pluripotency factors, increased expression of cell-lineage-affiliated developmental regulators, and induced cell morphological and biochemical changes indicative of ESC differentiation. Selective downregulation of pluripotency factors upon Spt6 depletion may be mechanistically explained by its enrichment at ESC super-enhancers, where Spt6 controls histone H3K27 acetylation and methylation and super-enhancer RNA transcription...
October 10, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29033289/foldability-of-a-natural-de-novo-evolved-protein
#11
Dixie Bungard, Jacob S Copple, Jing Yan, Jimmy J Chhun, Vlad K Kumirov, Scott G Foy, Joanna Masel, Vicki H Wysocki, Matthew H J Cordes
The de novo evolution of protein-coding genes from noncoding DNA is emerging as a source of molecular innovation in biology. Studies of random sequence libraries, however, suggest that young de novo proteins will not fold into compact, specific structures typical of native globular proteins. Here we show that Bsc4, a functional, natural de novo protein encoded by a gene that evolved recently from noncoding DNA in the yeast S. cerevisiae, folds to a partially specific three-dimensional structure. Bsc4 forms soluble, compact oligomers with high β sheet content and a hydrophobic core, and undergoes cooperative, reversible denaturation...
October 7, 2017: Structure
https://www.readbyqxmd.com/read/29033286/botulinum-toxins-a-and-e-inflict-dynamic-destabilization-on-t-snare-to-impair-snare-assembly-and-membrane-fusion
#12
Ryan Khounlo, Jaewook Kim, Linxiang Yin, Yeon-Kyun Shin
Botulinum toxins (BoNTs) A and E block neurotransmitter release by specifically cleaving the C- terminal ends of SNAP-25, a plasma membrane SNARE protein. Here, we find that SNAP-25A and E, the cleavage products of BoNT A and E, respectively, terminate membrane fusion via completely different mechanisms. Combined studies of single-molecule FRET and single-vesicle fusion assays reveal that SNAP-25E is incapable of supporting SNARE pairing and thus, vesicle docking. In contrast, SNAP-25A facilitates robust SNARE pairing and vesicle docking with somewhat reduced SNARE zippering, which leads to severe impairment of fusion pore opening...
October 4, 2017: Structure
https://www.readbyqxmd.com/read/29031730/bidirectional-manipulation-of-gene-expression-in-adipocytes-using-crispra-and-sirna
#13
Morten Lundh, Kaja Pluciñska, Marie S Isidor, Patricia S S Petersen, Brice Emanuelli
OBJECTIVE: Functional investigation of novel gene/protein targets associated with adipocyte differentiation or function heavily relies on efficient and accessible tools to manipulate gene expression in adipocytes in vitro. Recent advances in gene-editing technologies such as CRISPR-Cas9 have not only eased gene editing but also greatly facilitated modulation of gene expression without altering the genome. Here, we aimed to develop and validate a competent in vitro adipocyte model of controllable functionality as well as multiplexed gene manipulation in adipocytes, using the CRISPRa "SAM" system and siRNAs to simultaneously overexpress and silence selected genes in the same cell populations...
October 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/29031180/design-of-silk-proteins-with-increased-heme-binding-capacity-and-fabrication-of-silk-heme-materials
#14
Trevor D Rapson, Jian-Wei Liu, Alagacone Sriskantha, Mustafa Musameh, Christopher J Dunn, Jeffrey S Church, Andrea Woodhead, Andrew C Warden, Mark J Riley, Jeffrey R Harmer, Christopher J Noble, Tara D Sutherland
In our previous studies, heme was bound into honeybee silk to generate materials that could function as nitric oxide sensors or as recoverable heterogeneous biocatalysts. In this study, we sought to increase the heme-binding capacity of the silk protein by firstly redesigning the heme binding site to contain histidine as the coordinating residue and secondly, by adding multiple histidine residues within the core of the coiled coil core region of the modified silk protein. We used detergent and a protein denaturant to confirm the importance of the helical structure of the silk for heme coordination...
September 4, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/29031071/discovery-of-thienopyrrolotriazine-derivatives-to-protect-mitochondrial-function-against-a%C3%AE-induced-neurotoxicity
#15
TaeHun Kim, Woo Seung Son, Mohammad Neaz Morshed, Ashwini M Londhe, Seo Yun Jung, Jong-Hyun Park, Woo-Kyu Park, Sang Min Lim, Ki Duk Park, Sung Jin Cho, Kyu-Sung Jeong, Jiyoun Lee, Ae Nim Pae
Recovery of mitochondrial dysfunction has gained increasing attention as an alternative therapeutic strategy for Alzheimer's disease (AD). Recent studies suggested that the 18 kDa mitochondrial translocator protein (TSPO) has the potential to serve as a drug target for the treatment of AD. In this study, we generated a structure-based pharmacophore model and virtually screened a commercial library, identifying SVH07 as a virtual hit, which contained a tricyclic core structure, thieno[2',3':4,5]pyrrolo[1,2-d][1,2,4]triazine group...
September 21, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29030846/reconstitution-of-rna-interference-machinery
#16
Shintaro Iwasaki, Yukihide Tomari
Small RNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), silence protein expression from target mRNAs bearing their complementary sequences, via the formation of the effector complex called RNA-induced silencing complex (RISC). Although the mechanism of RISC assembly has been studied for nearly two decades, the detailed mechanism has still remained unclear in part due to the lack of a pure reconstitution system. Recently, we identified all the core proteins necessary for RISC assembly in flies and successfully recapitulated the assembly of catalytically active RISC with eight recombinant proteins...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29030613/lipopolysaccharide-enters-the-rat-brain-by-a-lipoprotein-mediated-transport-mechanism-in-physiological-conditions
#17
Alejandra Vargas-Caraveo, Aline Sayd, Sandra R Maus, Javier R Caso, José L M Madrigal, Borja García-Bueno, Juan C Leza
Physiologically, lipopolysaccharide (LPS) is present in the bloodstream and can be bound to several proteins for its transport (i.e.) LPS binding protein (LBP) and plasma lipoproteins). LPS receptors CD14 and TLR-4 are constitutively expressed in the Central Nervous System (CNS). To our knowledge, LPS infiltration in CNS has not been clearly demonstrated. A naturalistic experiment with healthy rats was performed to investigate whether LPS is present with its receptors in brain. Immunofluorescences showed that lipid A and core LPS were present in circumventricular organs, choroid plexus, meningeal cells, astrocytes, tanycytes and endothelial cells...
October 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29030390/apc-c-fzr-1-controls-sas-5-levels-to-regulate-centrosome-duplication-in-caenorhabditis-elegans
#18
Jeffrey C Medley, Lauren E DeMeyer, Megan M Kabara, Mi Hye Song
As the primary microtubule-organizing center, centrosomes play a key role in establishing mitotic bipolar spindles that secure correct transmission of genomic content. For the fidelity of cell division, centrosome number must be strictly controlled by duplicating only once per cell cycle. Proper levels of centrosome proteins are shown to be critical for normal centrosome number and function. Overexpressing core centrosome factors leads to extra centrosomes, while depleting these factors results in centrosome duplication failure...
October 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29030303/electrospun-formulations-of-bevacizumab-for-sustained-release-in-the-eye
#19
Ukrit Angkawinitwong, Sahar Awwad, Peng T Khaw, Steve Brocchini, Gareth R Williams
Medicines based on vascular endothelial growth factor (VEGF) neutralising antibodies such as bevacizumab have revolutionized the treatment of age related macular degeneration (AMD), a common blinding disease, and have great potential in preventing scarring after surgery or accelerating the healing of corneal injuries. However, at present, frequent invasive injections are required to deliver these antibodies. Such administration is uncomfortable for patients and expensive for health service providers. Much effort is thus focused on developing dosage forms that can be administered less frequently...
October 10, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/29029784/regulation-of-insulin-exocytosis-by-calcium-dependent-protein-kinase-c-in-beta-cells
#20
REVIEW
Adam J Trexler, Justin W Taraska
The control of insulin release from pancreatic beta cells helps ensure proper blood glucose level, which is critical for human health. Protein kinase C has been shown to be one key control mechanism for this process. After glucose stimulation, calcium influx into beta cells triggers exocytosis of insulin-containing dense-core granules and activates protein kinase C via calcium-dependent phospholipase C-mediated generation of diacylglycerol. Activated protein kinase C potentiates insulin release by enhancing the calcium sensitivity of exocytosis, likely by affecting two main pathways that could be linked: (1) the reorganization of the cortical actin network, and (2) the direct phosphorylation of critical exocytotic proteins such as munc18, SNAP25, and synaptotagmin...
November 2017: Cell Calcium
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