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FAD binding protein

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https://www.readbyqxmd.com/read/27901000/endoplasmic-reticulum-stress-induces-the-early-appearance-of-pro-apoptotic-and-anti-apoptotic-proteins-in-neurons-of-five-familial-alzheimer-s-disease-mice
#1
Hui Shen, Xiao-Dong Pan, Jing Zhang, Yu-Qi Zeng, Meng Zhou, Lu-Meng Yang, Bing Ye, Xiao-Man Dai, Yuan-Gui Zhu, Xiao-Chun Chen
BACKGROUND: Amyloid β (Aβ) deposits and the endoplasmic reticulum stress (ERS) are both well established in the development and progression of Alzheimer's disease (AD). However, the mechanism and role of Aβ-induced ERS in AD-associated pathological progression remain to be elucidated. METHODS: The five familial AD (5×FAD) mice and wild-type (WT) mice aged 2, 7, and 12 months were used in the present study. Morris water maze test was used to evaluate their cognitive performance...
2016: Chinese Medical Journal
https://www.readbyqxmd.com/read/27864152/the-flavinyl-transferase-apbe-of-pseudomonas-stutzeri-matures-the-nosr-protein-required-for-nitrous-oxide-reduction
#2
Lin Zhang, Christian Trncik, Susana L A Andrade, Oliver Einsle
The copper-containing enzyme nitrous oxide reductase (N2OR) catalyzes the transformation of nitrous oxide (N2O) to dinitrogen (N2) in microbial denitrification. Several accessory factors are essential for assembling the two copper sites CuA and CuZ and for maintaining their activity. In particular, the deletion of either the transmembrane iron-sulfur flavoprotein NosR or the periplasmic protein NosX, a member of the ApbE family, abolishes N2O respiration. Here we demonstrate through biochemical and structural studies that the ApbE protein from Pseudomonas stutzeri, where the nosX gene is absent, is a monomeric FAD-binding protein that can serve as the flavin donor for NosR maturation via covalent flavinylation of a threonine residue...
November 15, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27845672/gpu-based-point-cloud-superpositioning-for-structural-comparisons-of-protein-binding-sites
#3
Matthias Leinweber, Thomas Fober, Bernd Freisleben
In this paper, we present a novel approach to solve the labeled point cloud superpositioning problem for performing structural comparisons of protein binding sites. The solution is based on a parallel evolution strategy that operates on large populations and runs on GPU hardware. The proposed evolution strategy reduces the likelihood of getting stuck in a local optimum of the multimodal real-valued optimization problem represented by labeled point cloud superpositioning. The performance of the GPU-based parallel evolution strategy is compared to a previously proposed CPU-based sequential approach for labeled point cloud superpositioning, indicating that the GPU-based parallel evolution strategy leads to qualitatively better results and significantly shorter runtimes, with speed improvements of up to a factor of 1,500 for large populations...
November 7, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27830466/engineering-styrene-monooxygenase-for-biocatalysis-reductase-epoxidase-fusion-proteins
#4
Thomas Heine, Kathryn Tucker, Nonye Okonkwo, Berhanegebriel Assefa, Catleen Conrad, Anika Scholtissek, Michael Schlömann, George Gassner, Dirk Tischler
The enantioselective epoxidation of styrene and related compounds by two-component styrene monooxygenases (SMOs) has targeted these enzymes for development as biocatalysts. In the present work, we prepare genetically engineered fusion proteins that join the C-terminus of the epoxidase (StyA) to the N-terminus of the reductase (StyB) through a linker peptide and demonstrate their utility as biocatalysts in the synthesis of Tyrain purple and other indigoid dyes. A single-vector expression system offers a simplified platform for transformation and expansion of the catalytic function of styrene monooxygenases, and the resulting fusion proteins are self-regulated and couple efficiently NADH oxidation to styrene epoxidation...
November 9, 2016: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/27760350/stimulation-of-nipah-fusion-small-intradomain-changes-trigger-extensive-interdomain-rearrangements
#5
Priyanka Dutta, Ahnaf Siddiqui, Mohsen Botlani, Sameer Varma
Nipah is an emerging paramyxovirus that is of serious concern to human health. It invades host cells using two of its membrane proteins-G and F. G binds to host ephrins and this stimulates G to activate F. Upon activation, F mediates virus-host membrane fusion. Here we focus on mechanisms that underlie the stimulation of G by ephrins. Experiments show that G interacts with ephrin and F through separate sites located on two different domains, the receptor binding domain (RBD) and the F activation domain (FAD)...
October 18, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27745833/variants-in-the-oxidoreductase-pyroxd1-cause-early-onset-myopathy-with-internalized-nuclei-and-myofibrillar-disorganization
#6
Gina L O'Grady, Heather A Best, Tamar E Sztal, Vanessa Schartner, Myriam Sanjuan-Vazquez, Sandra Donkervoort, Osorio Abath Neto, Roger Bryan Sutton, Biljana Ilkovski, Norma Beatriz Romero, Tanya Stojkovic, Jahannaz Dastgir, Leigh B Waddell, Anne Boland, Ying Hu, Caitlin Williams, Avnika A Ruparelia, Thierry Maisonobe, Anthony J Peduto, Stephen W Reddel, Monkol Lek, Taru Tukiainen, Beryl B Cummings, Himanshu Joshi, Juliette Nectoux, Susan Brammah, Jean-François Deleuze, Viola Oorschot Ing, Georg Ramm, Didem Ardicli, Kristen J Nowak, Beril Talim, Haluk Topaloglu, Nigel G Laing, Kathryn N North, Daniel G MacArthur, Sylvie Friant, Nigel F Clarke, Robert J Bryson-Richardson, Carsten G Bönnemann, Jocelyn Laporte, Sandra T Cooper
This study establishes PYROXD1 variants as a cause of early-onset myopathy and uses biospecimens and cell lines, yeast, and zebrafish models to elucidate the fundamental role of PYROXD1 in skeletal muscle. Exome sequencing identified recessive variants in PYROXD1 in nine probands from five families. Affected individuals presented in infancy or childhood with slowly progressive proximal and distal weakness, facial weakness, nasal speech, swallowing difficulties, and normal to moderately elevated creatine kinase...
November 3, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27739235/rhodobacter-sphaeroides-cryb-is-a-bacterial-cryptochrome-with-6-4-photolyase-activity
#7
Andrea von Zadow, Elisabeth Ignatz, Richard Pokorny, Lars-Oliver Essen, Gabriele Klug
Photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers or (6-4) photoproducts in a light-dependent cleavage reaction. The closely related classical cryptochrome blue light photoreceptors do not repair DNA lesions; instead they are involved in regulatory processes. CryB of Rhodobacter sphaeroides was until now described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition...
October 14, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27640649/the-mir-33-gene-is-identified-in-a-marine-teleost-a-potential-role-in-regulation-of-lc-pufa-biosynthesis-in-siganus-canaliculatus
#8
Qinghao Zhang, Cuihong You, Shuqi Wang, Yewei Dong, Óscar Monroig, Douglas R Tocher, Yuanyou Li
As the first marine teleost demonstrated to have the ability to biosynthesize long-chain polyunsaturated fatty acids (LC-PUFA) from C18 PUFA precursors, rabbitfish Siganus canaliculatus provides a good model for studying the regulatory mechanisms of LC-PUFA biosynthesis in teleosts. Here the potential roles of miR-33 in such regulation were investigated. The miR-33 gene was identified within intron 16 of the gene encoding sterol regulatory element-binding protein 1 (Srebp1), an activator of LC-PUFA biosynthesis...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27625790/alzheimer-s-disease-associated-mutations-increase-amyloid-precursor-protein-resistance-to-%C3%AE-secretase-cleavage-and-the-a%C3%AE-42-a%C3%AE-40-ratio
#9
Ting-Hai Xu, Yan Yan, Yanyong Kang, Yi Jiang, Karsten Melcher, H Eric Xu
Mutations in the amyloid precursor protein (APP) gene and the aberrant cleavage of APP by γ-secretase are associated with Alzheimer's disease (AD). Here we have developed a simple and sensitive cell-based assay to detect APP cleavage by γ-secretase. Unexpectedly, most familial AD (FAD)-linked APP mutations make APP partially resistant to γ-secretase. Mutations that alter residues N terminal to the γ-secretase cleavage site Aβ42 have subtle effects on cleavage efficiency and cleavage-site selectivity. In contrast, mutations that alter residues C terminal to the Aβ42 site reduce cleavage efficiency and dramatically shift cleavage-site specificity toward the aggregation-prone Aβ42...
2016: Cell Discovery
https://www.readbyqxmd.com/read/27592049/the-sequence-variation-and-functional-differentiation-of-crds-in-a-scallop-multiple-crds-containing-lectin
#10
Mengmeng Huang, Lingling Wang, Huan Zhang, Chuanyan Yang, Rui Liu, Jiachao Xu, Zhihao Jia, Linsheng Song
A C-type lectin of multiple CRDs (CfLec-4) from Chlamys farreri was selected to investigate the sequence variation and functional differentiation of its CRDs. Its four CRDs with EPD/LSD, EPN/FAD, EPN/LND and EPN/YND key motifs were recombined separately. The recombinant proteins of CRD1 and CRD2 (designated as rCRD1 and rCRD2) could bind LPS and mannan, while the recombinant proteins of CRD3 and CRD4 (designated as rCRD3 and rCRD4) could bind LPS, PGN, mannan and glucan. Moreover, rCRD3 displayed broad microbe binding spectrum towards Gram-positive bacteria Staphylococcus aureus and Micrococcus luteus, Gram-negative bacteria Escherichia coli and Vibrio anguillarum, as well as fungi Pichia pastoris and Yarrowia lipolytica...
August 31, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27590343/a-novel-f420-dependent-thioredoxin-reductase-gated-by-low-potential-fad-a-tool-for-redox-regulation-in-an-anaerobe
#11
Dwi Susanti, Usha Loganathan, Biswarup Mukhopadhyay
A recent report suggested that the thioredoxin-dependent metabolic regulation, which is widespread in all domains of life, existed in methanogenic archaea about 3.5 billion years ago. We now show that the respective electron delivery enzyme (thioredoxin reductase, TrxR), although structurally similar to flavin-containing NADPH-dependent TrxRs (NTR), lacked an NADPH-binding site and was dependent on reduced coenzyme F420 (F420H2), a stronger reductant with a mid-point redox potential (E'0) of -360 mV; E'0 of NAD(P)H is -320 mV...
October 28, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27580869/structure-based-classification-of-fad-binding-sites-a-comparative-study-of-structural-alignment-tools-comparison-and-classification-of-fad-binding-sites
#12
Leonardo D Garma, Milagros Medina, André H Juffer
A total of six different structural alignment tools (TM-Align, TriangleMatch, CLICK, ProBis, SiteEngine and GA-SI) were assessed for their ability to perform two particular tasks: (i) discriminating FAD (flavin adenine dinucleotide) from non-FAD binding sites, and (ii) performing an all-to-all comparison on a set of 883 FAD binding sites with the purpose of classifying them. For the first task, the consistency of each alignment method was evaluated, showing that every method is able to distinguish FAD and non-FAD binding sites with a high Matthews correlation coefficient...
September 1, 2016: Proteins
https://www.readbyqxmd.com/read/27577995/renalase-secreted-by-human-kidney-hek293t-cells-lacks-its-n-terminal-peptide-implications-for-putative-mechanisms-of-renalase-action
#13
Valerii Fedchenko, Arthur Kopylov, Nadezhda Kozlova, Olga Buneeva, Alexei Kaloshin, Victor Zgoda, Alexei Medvedev
BACKGROUND/AIMS: Renalase is a recently discovered flavoprotein involved in regulation of blood pressure. Altered renalase levels have been found in blood of patients with end stage renal disease. The antihypertensive effect of circulating renalase is attributed to putative FAD-dependent monoamine oxidase activity demonstrated by some authors. Being synthesized as an intracellular flavoprotein renalase requires the presence of its N-terminal peptide for FAD accommodation. However, conventional routes of export of secretory proteins outside the cell usually include cleavage of their N-terminal peptide...
2016: Kidney & Blood Pressure Research
https://www.readbyqxmd.com/read/27563493/correlating-calmodulin-landscapes-with-chemical-catalysis-in-neuronal-nitric-oxide-synthase-using-time-resolved-fret-and-a-5-deazaflavin-thermodynamic-trap
#14
Tobias M Hedison, Nicole G H Leferink, Sam Hay, Nigel S Scrutton
A major challenge in enzymology is the need to correlate the dynamic properties of enzymes with, and understand the impact on, their catalytic cycles. This is especially the case with large, multicenter enzymes such as the nitric oxide synthases (NOSs), where the importance of dynamics has been inferred from a variety of structural, single-molecule, and ensemble spectroscopic approaches but where motions have not been correlated experimentally with mechanistic steps in the reaction cycle. Here we take such an approach...
August 5, 2016: ACS Catalysis
https://www.readbyqxmd.com/read/27560664/validation-of-reference-genes-for-robust-qrt-pcr-gene-expression-analysis-in-the-rice-blast-fungus-magnaporthe-oryzae
#15
Sarena Che Omar, Michael A Bentley, Giulia Morieri, Gail M Preston, Sarah J Gurr
The rice blast fungus causes significant annual harvest losses. It also serves as a genetically-tractable model to study fungal ingress. Whilst pathogenicity determinants have been unmasked and changes in global gene expression described, we know little about Magnaporthe oryzae cell wall remodelling. Our interests, in wall remodelling genes expressed during infection, vegetative growth and under exogenous wall stress, demand robust choice of reference genes for quantitative Real Time-PCR (qRT-PCR) data normalisation...
2016: PloS One
https://www.readbyqxmd.com/read/27560143/crystal-structures-of-sgce6-and-sgcc-the-two-component-monooxygenase-that-catalyzes-hydroxylation-of-a-carrier-protein-tethered-substrate-during-the-biosynthesis-of-the-enediyne-antitumor-antibiotic-c-1027-in-streptomyces-globisporus
#16
Chin-Yuan Chang, Jeremy R Lohman, Hongnan Cao, Kemin Tan, Jeffrey D Rudolf, Ming Ma, Weijun Xu, Craig A Bingman, Ragothaman M Yennamalli, Lance Bigelow, Gyorgy Babnigg, Xiaohui Yan, Andrzej Joachimiak, George N Phillips, Ben Shen
C-1027 is a chromoprotein enediyne antitumor antibiotic produced by Streptomyces globisporus. In the last step of biosynthesis of the (S)-3-chloro-5-hydroxy-β-tyrosine moiety of the C-1027 enediyne chromophore, SgcE6 and SgcC compose a two-component monooxygenase that hydroxylates the C-5 position of (S)-3-chloro-β-tyrosine. This two-component monooxygenase is remarkable for two reasons. (i) SgcE6 specifically reacts with FAD and NADH, and (ii) SgcC is active with only the peptidyl carrier protein (PCP)-tethered substrate...
September 13, 2016: Biochemistry
https://www.readbyqxmd.com/read/27557658/the-structure-of-the-antibiotic-deactivating-n-hydroxylating-rifampicin-monooxygenase
#17
Li-Kai Liu, Heba Abdelwahab, Julia S Martin Del Campo, Ritcha Mehra-Chaudhary, Pablo Sobrado, John J Tanner
Rifampicin monooxygenase (RIFMO) catalyzes the N-hydroxylation of the natural product antibiotic rifampicin (RIF) to 2'-N-hydroxy-4-oxo-rifampicin, a metabolite with much lower antimicrobial activity. RIFMO shares moderate sequence similarity with well characterized flavoprotein monooxygenases, but the protein has not been isolated and characterized at the molecular level. Herein, we report crystal structures of RIFMO from Nocardia farcinica, the determination of the oligomeric state in solution with small angle x-ray scattering, and the spectrophotometric characterization of substrate binding...
October 7, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27539124/characterization-of-myma-protein-as-a-flavin-containing-monooxygenase-and-as-a-target-of-isoniazid
#18
Iti Saraav, Kirti Pandey, Richa Misra, Swati Singh, Monika Sharma, Sadhna Sharma
Tuberculosis is a global health problem especially with emergence of drug resistant Mycobacterium tuberculosis strains, creating an urgent need to identify new drug targets. The mycobacterial cell wall is an attractive target for chemotherapeutic agents. Gene products of mymA operon are known to be required for maintenance of cell wall and play an important role in persistence, thus making them important drug targets. The present study was undertaken to biochemically characterize the MymA as a Flavin Containing Monooxygenase (FMO)...
August 19, 2016: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/27475771/prediction-of-fad-binding-sites-in-electron-transport-proteins-according-to-efficient-radial-basis-function-networks-and-significant-amino-acid-pairs
#19
Nguyen-Quoc-Khanh Le, Yu-Yen Ou
BACKGROUND: Cellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food. When cells undergo cellular respiration, they require a pathway to keep and transfer electrons (i.e., the electron transport chain). Due to oxidation-reduction reactions, the electron transport chain produces a transmembrane proton electrochemical gradient. In case protons flow back through this membrane, this mechanical energy is converted into chemical energy by ATP synthase...
2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27472219/hepatocyte-nuclear-factor-4%C3%AE-hnf4%C3%AE-is-a-transcription-factor-of-vertebrate-fatty-acyl-desaturase-gene-as-identified-in-marine-teleost-siganus-canaliculatus
#20
Yewei Dong, Shuqi Wang, Junliang Chen, Qinghao Zhang, Yang Liu, Cuihong You, Óscar Monroig, Douglas R Tocher, Yuanyou Li
Rabbitfish Siganus canaliculatus was the first marine teleost demonstrated to have the capability of biosynthesizing long-chain polyunsaturated fatty acids (LC-PUFA) from C18 precursors, and to possess a Δ4 fatty acyl desaturase (Δ4 Fad) which was the first report in vertebrates, and is a good model for studying the regulatory mechanisms of LC-PUFA biosynthesis in teleosts. In order to understand regulatory mechanisms of transcription of Δ4 Fad, the gene promoter was cloned and characterized in the present study...
2016: PloS One
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