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endo loop

Davide Moiani, Daryl A Ronato, Chris A Brosey, Andrew S Arvai, Aleem Syed, Jean-Yves Masson, Elena Petricci, John A Tainer
For inhibitor design, as in most research, the best system is question dependent. We suggest structurally defined allostery to design specific inhibitors that target regions beyond active sites. We choose systems allowing efficient quality structures with conformational changes as optimal for structure-based design to optimize inhibitors. We maintain that evolutionarily related targets logically provide molecular avatars, where this Sanskrit term for descent includes ideas of functional relationships and of being a physical embodiment of the target's essential features without requiring high sequence identity...
2018: Methods in Enzymology
Wanju Jiao, Yajun Chen, Huajie Song, Dan Li, Hong Mei, Feng Yang, Erhu Fang, Xiaojing Wang, Kai Huang, Liduan Zheng, Qiangsong Tong
Recent studies reveal the emerging functions of enhancer RNAs (eRNAs) in gene expression. However, the roles of eRNAs in regulating the expression of heparanase (HPSE), an established endo-β-D-glucuronidase essential for cancer invasion and metastasis, still remain elusive. Herein, through comprehensive analysis of publically available FANTOM5 expression atlas and chromatin interaction dataset, we identified a super enhancer and its derived eRNA facilitating the HPSE expression (HPSE eRNA) in cancers. Gain-of-function and loss-of-function experiments indicated that HPSE eRNA facilitated the in vitro and in vivo tumorigenesis and aggressiveness of cancer cells...
March 7, 2018: Oncogene
Aleksandar Spasic, Scott D Kennedy, Laura Needham, Muthiah Manoharan, Ryszard Kierzek, Douglas H Turner, David Mathews
The RNA "GAGU" duplex, (5'GACGAGUGUCA)2, contains the internal loop (5'-GAGU-3')2 , which has two conformations in solution as determined by NMR spectroscopy. The major conformation has a loop structure consisting of trans-Watson-Crick/Hoogsteen GG pairs, two A residues stacked on each other, two U residues bulged outside the helix and exposed to solvent, and all sugars with a C2'-endo conformation. This differs markedly from the internal loops, (5'-GAGC-3')2 , (5'-AAGU-3')2 and (5'-UAGG-3')2, which all have cis-Watson-Crick/Watson-Crick AG "imino" non-canonical pairs flanked by cis Watson-Crick/Watson-Crick canonical pairs resulting in maximal hydrogen bonding...
February 6, 2018: RNA
Stine A Mikkelsen, Peter Vangheluwe, Jens Peter Andersen
The sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) 2b isoform possesses an extended C terminus (SERCA2b tail) forming an 11th transmembrane (TM) helix, which slows conformational changes of the Ca2+-pump reaction cycle. Here, we report that a Darier disease (DD) mutation of SERCA2b that changes a glutamate to lysine in the cytoplasmic loop between TM8 and TM9 (E917K) relieves these kinetic constraints. We analyzed the effects of this mutation on the overall reaction and the individual partial reactions of the Ca2+ pump compared with the corresponding mutations of the SERCA2a and SERCA1a isoforms lacking the SERCA2b tail...
January 23, 2018: Journal of Biological Chemistry
Ho Namkoong, Masahiko Yamazaki, Masami Ishizaki, Ikumi Endo, Noriaki Harada, Megumi Aramaki, Yuko Tanaka, Sachiko Kaburagi, Masataka Ichikawa, Takanori Ohata, Shinji Sakaguchi, Fumitake Saito, Ayumi Nakao, Hideki Yuki, Keiko Mitamura
Mycoplasma pneumoniae infection is conventionally diagnosed using serum antibody testing, microbial culture, and genetic testing. Recently, immunochromatography-based rapid mycoplasma antigen test kits have been developed and commercialised for rapid diagnosis of M. pneumoniae infection. However, as these kits do not provide sufficient sensitivity and specificity, a rapid test kit with improved accuracy is desired. The present prospective study evaluated a rapid M. pneumoniae diagnostic system utilizing a newly developed silver amplification immunochromatography (SAI) system...
January 23, 2018: Scientific Reports
Anna S Borisova, Elena V Eneyskaya, Suvamay Jana, Silke F Badino, Jeppe Kari, Antonella Amore, Magnus Karlsson, Henrik Hansson, Mats Sandgren, Michael E Himmel, Peter Westh, Christina M Payne, Anna A Kulminskaya, Jerry Ståhlberg
Background: The ascomycete fungus Trichoderma reesei is the predominant source of enzymes for industrial conversion of lignocellulose. Its glycoside hydrolase family 7 cellobiohydrolase (GH7 CBH) TreCel7A constitutes nearly half of the enzyme cocktail by weight and is the major workhorse in the cellulose hydrolysis process. The orthologs from Trichoderma atroviride (TatCel7A) and Trichoderma harzianum (ThaCel7A) show high sequence identity with TreCel7A, ~ 80%, and represent naturally evolved combinations of cellulose-binding tunnel-enclosing loop motifs, which have been suggested to influence intrinsic cellobiohydrolase properties, such as endo-initiation, processivity, and off-rate...
2018: Biotechnology for Biofuels
Yuan Zhang, Christopher Roland, Celeste Sagui
A (GGGGCC) hexanucleotide repeat (HR) expansion in the C9ORF72 gene has been considered the major cause behind both frontotemporal dementia and amyotrophic lateral sclerosis, while a (GGGCCT) is associated with spinocerebellar ataxia 36. Recent experiments involving NMR, CD, optical melting and 1D1 H NMR spectroscopy, suggest that the r(GGGGCC) HR can adopt a hairpin structure with G-G mismatches in equilibrium with a G-quadruplex structure. G-Quadruplexes have also been identified for d(GGGGCC). As these experiments lack molecular resolution, we have used molecular dynamics microsecond simulations to obtain a structural characterization of the G-quadruplexes associated with both HRs...
January 12, 2018: ACS Chemical Neuroscience
Marc Simard, Caroline Underhill, Geoffrey L Hammond
Corticosteroid-binding globulin (CBG) is a plasma carrier of glucocorticoids. Human and rat CBGs have six N-glycosylation sites. Glycosylation of human CBG influences its steroid-binding activity and there are N-glycosylation sites in the reactive center loops (RCLs) of human and rat CBGs. Proteolysis of the RCL of human CBG causes a structural change that disrupts steroid binding. We now show that mutations of conserved N-glycosylation sites at N238 in human CBG and N230 in rat CBG disrupt steroid binding...
December 22, 2017: Journal of Molecular Endocrinology
Xin Liu, Tengfei Liu, Yuebin Zhang, Fengjiao Xin, Shuofu Mi, Boting Wen, Tianyi Gu, Xinyuan Shi, Fengzhong Wang, Lichao Sun
Xylanase (EC is a kind of enzymes that degrade xylan into xylose, which has been widely used in a variety of industrial applications. Particularly, xylanases from thermophilic microorganisms show distinct advantages in the industries which need high temperature conditions. The CoXynA gene, which is identified from thermophilic bacterium Caldicellulosiruptor owensensis, encoding a glycoside hydrolase family 10 xylanase, was overexpressed in Escherichia coli. The recombinant CoXynA showed optimal activity at 90°C and pH 7...
December 13, 2017: Journal of Agricultural and Food Chemistry
Keisuke Inoue, Takashi Araki, Motomu Endo
Plants have endogenous biological clocks that allow organisms to anticipate and prepare for daily and seasonal environmental changes and increase their fitness in changing environments. The circadian clock in plants, as in animals and insects, mainly consists of multiple interlocking transcriptional/translational feedback loops. The circadian clock can be entrained by environmental cues such as light, temperature and nutrient status to synchronize internal biological rhythms with surrounding environments. Output pathways link the circadian oscillator to various physiological, developmental, and reproductive processes for adjusting the timing of these biological processes to an appropriate time of day or a suitable season...
November 13, 2017: Journal of Plant Research
Shiho Tanaka, Haruka Endo, Satomi Adegawa, Ami Iizuka, Kazuhiro Imamura, Shingo Kikuta, Ryoichi Sato
Because Bombyx mori ABC transporter C2 (BmABCC2) has 1000-fold higher potential than B. mori cadherin-like protein as a receptor for Bacillus thuringiensis Cry1Aa toxin (Tanaka et al., 2013), the gate-opening ability of the latent pore under six extracellular loops (ECLs) of BmABCC2 was expected to be the reason for its higher potential (Heckel, 2012). In this study, cell swelling assays in Sf9 cells showed that BmABCC2 mutants lacking substrate-excreting activity retained receptor activity, indicating that the gate-opening activity of BmABCC2 is not responsible for Cry1Aa toxicity...
December 2017: Insect Biochemistry and Molecular Biology
Flemming Javier Olsen, Jesper Hastrup Svendsen, Lars Køber, Søren Højberg, Ketil Haugan, Jan Skov Jensen, Tor Biering-Sørensen
Speckle tracking echocardiography is an emerging technique, which is currently being included in clinical guidelines. We sought to investigate the impact of transducer frequency settings on speckle tracking derived measures. The study comprised of 22 subjects prospectively enrolled for a randomized controlled trial (LOOP-study, Patients were above 70 years of age with increased risk of stroke, and had an echocardiogram performed, which included focused images of the left ventricle...
November 3, 2017: International Journal of Cardiovascular Imaging
Marianna Truman-Rosentsvit, Dina Berenbaum, Lior Spektor, Lyora A Cohen, Shirly Belizowsky-Moshe, Lena Lifshitz, Jing Ma, Wei Li, Ellina Kesselman, Inbal Abutbul-Ionita, Dganit Danino, Lucia Gutierrez, Huihui Li, Kuanyu Li, Huifang Lou, Maria Regoni, Maura Poli, Fabian Glaser, Tracey A Rouault, Esther G Meyron-Holtz
Ferritin turnover plays a major role in tissue iron homeostasis, and ferritin malfunction is associated with impaired iron homeostasis and neurodegenerative diseases. In most eukaryotes, ferritin is considered an intracellular protein that stores iron in a nontoxic and bioavailable form. In insects, ferritin is a classically secreted protein and plays a major role in systemic iron distribution. Mammalian ferritin lacks the signal peptide for classical endoplasmic reticulum-Golgi secretion but is found in serum and is secreted via a nonclassical lysosomal secretion pathway...
January 18, 2018: Blood
Kohsuke Shirakawa, Jin Endo, Yoshinori Katsumata, Tsunehisa Yamamoto, Masaharu Kataoka, Sarasa Isobe, Naohiro Yoshida, Keiichi Fukuda, Motoaki Sano
Obesity promotes excessive inflammation, which is associated with senescence-like changes in visceral adipose tissue (VAT) and the development of type 2 diabetes (T2DM) and cardiovascular diseases. We have reported that a unique population of CD44hi CD62Llo CD4+ T cells that constitutively express PD-1 and CD153 exhibit cellular senescence and cause VAT inflammation by producing large amounts of osteopontin. Weight loss improves glycemic control and reduces cardiovascular disease risk factors, but its long-term effects on cardiovascular events and longevity in obese individuals with T2DM are somewhat disappointing and not well understood...
2017: PloS One
Wenfang Du, Junjie Li, Fubing Xiao, Ruqin Yu, Jianhui Jiang
Uracil-DNA glycosylase (UDG) plays essential roles in base excision repair (BER) pathway by eliminating uracil from DNA to sustain the genome integrity. Sensitive detection of UDG activity is of great significance in the study of many fundamental biochemical processes and clinical applications. We develop a label-free method for UDG activity detection using stem-loop primer-mediated exponential amplification (SPEA). In the presence of active UDG, the uracil base in helper hairpin probe (HP) can be excised to generate an abasic site (AP site), which can be cleaved by endonuclease IV (Endo IV) with a blocked primer released...
October 23, 2017: Analytica Chimica Acta
Navin Gopaldass, Bruno Fauvet, Hilal Lashuel, Aurélien Roux, Andreas Mayer
Sorting, transport, and autophagic degradation of proteins in endosomes and lysosomes, as well as the division of these organelles, depend on scission of membrane-bound tubulo-vesicular carriers. How scission occurs is poorly understood, but family proteins bind these membranes. Here, we show that the yeast PROPPIN Atg18 carries membrane scission activity. Purified Atg18 drives tubulation and scission of giant unilamellar vesicles. Upon membrane contact, Atg18 folds its unstructured CD loop into an amphipathic α-helix that inserts into the bilayer...
November 15, 2017: EMBO Journal
Lavanya Tayi, Sushil Kumar, Rajkanwar Nathawat, Asfarul S Haque, Roshan V Maku, Hitendra Kumar Patel, Rajan Sankaranarayanan, Ramesh V Sonti
Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, a serious disease of rice. Xoo secretes a repertoire of cell wall degrading enzymes which includes cellulases, xylanases, pectinases to degrade various polysaccharide components of the rice cell wall. A secreted Xoo cellulase, CbsA, is not only a key virulence factor of Xoo but is also a potent inducer of innate immune responses of rice. In this study, we have solved the crystal structure of the catalytic domain of CbsA protein to a resolution of 1...
October 4, 2017: Molecular Plant Pathology
Clotilde Huet-Calderwood, Felix Rivera-Molina, Daniel V Iwamoto, Emil B Kromann, Derek Toomre, David A Calderwood
Integrins are abundant heterodimeric cell-surface adhesion receptors essential in multicellular organisms. Integrin function is dynamically modulated by endo-exocytic trafficking, however, major mysteries remain about where, when, and how this occurs in living cells. To address this, here we report the generation of functional recombinant β1 integrins with traceable tags inserted in an extracellular loop. We demonstrate that these 'ecto-tagged' integrins are cell-surface expressed, localize to adhesions, exhibit normal integrin activation, and restore adhesion in β1 integrin knockout fibroblasts...
September 18, 2017: Nature Communications
Eiki Kimura, Ken-Ichiro Kubo, Toshihiro Endo, Wenting Ling, Kazunori Nakajima, Masaki Kakeyama, Chiharu Tohyama
The basic helix-loop-helix (bHLH) transcription factors exert multiple functions in mammalian cerebral cortex development. The aryl hydrocarbon receptor (AhR), a member of the bHLH-Per-Arnt-Sim subfamily, is a ligand-activated transcription factor reported to regulate nervous system development in both invertebrates and vertebrates, but the functions that AhR signaling pathway may have for mammalian cerebral cortex development remains elusive. Although the endogenous ligand involved in brain developmental process has not been identified, the environmental pollutant dioxin potently binds AhR and induces abnormalities in higher brain function of laboratory animals...
2017: PloS One
Nora Gehne, Agathe Lamik, Martin Lehmann, Reiner F Haseloff, Anuska V Andjelkovic, Ingolf E Blasig
Claudins (Cldns) are transmembrane tight junction (TJ) proteins that paracellularly seal endo- and epithelial barriers by their interactions within the TJs. However, the mechanisms allowing TJ remodeling while maintaining barrier integrity are largely unknown. Cldns and occludin are heterophilically and homophilically cross-over endocytosed into neighboring cells in large, double membrane vesicles. Super-resolution microscopy confirmed the presence of Cldns in these vesicles and revealed a distinct separation of Cldns derived from opposing cells within cross-over endocytosed vesicles...
2017: PloS One
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