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FAD binding protein

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https://www.readbyqxmd.com/read/28091661/biochemical-characterization-of-the-selenoproteome-in-gallus-gallus-via-bioinformatics-analysis-structure-function-relationships-and-interactions-of-binding-molecules
#1
Shi-Yong Zhu, Xue-Nan Li, Xiao-Chen Sun, Jia Lin, Wei Li, Cong Zhang, Jin-Long Li
Knowledge about mammalian selenoproteins is increasing. However, the selenoproteome of birds remains considerably less understood, especially concerning its biochemical characterization, structure-function relationships and the interactions of binding molecules. In this work, the SECIS elements, subcellular localization, protein domains and interactions of binding molecules of the selenoproteome in Gallus gallus were analyzed using bioinformatics tools. We carried out comprehensive analyses of the structure-function relationships and interactions of the binding molecules of selenoproteins, to provide biochemical characterization of the selenoproteome in Gallus gallus...
January 16, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/27994211/proteome-changes-in-penicillium-expansum-grown-in-a-medium-derived-from-host-plant
#2
Xiaoshuang Xia, Huan Li, Fei Liu, Ye Zhang, Qi Zhang, Yun Wang, Peiwu Li
Penicillium expansum causes blue mould rot, a prevalent post-harvest disease of pome fruit, and is also the main producer of the patulin. However, knowledge on the molecular mechanisms involved in this pathogen-host interaction remains largely unknown. In this work, a two-dimensional gel electrophoresis (2-DE)-based proteomic approach was applied to probe changes in P. expansum cultivated in apple juice medium, which was used to mimic the in planta condition. The results showed that pH value and reducing sugar content in the apple juice medium decreased whereas the patulin content increased with the growing of P...
December 20, 2016: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27992645/crystal-structures-of-bacterial-6-4-photolyase-mutants-with-impaired-dna-repair-activity
#3
Fan Zhang, Hongju Ma, Kalinga Bowatte, Dennis Kwiatkowski, Esther Mittmann, Heba Qasem, Norbert Krauss, Xiaoli Zeng, Zhong Ren, Patrick Scheerer, Xiaojing Yang, Tilman Lamparter
PhrB from Agrobacterium fabrum is the first prokaryotic photolyase which repairs (6-4) UV DNA-photoproducts. The protein harbors three cofactors, the enzymatically active FAD chromophore, a second chromophore, 6,7-dimethyl-8-ribityllumazine (DMRL) and a cubane-type Fe-S cluster. Tyr424 of PhrB is part of the DNA binding site and could provide an electron link to the Fe-S cluster. The PhrBY424F mutant showed reduced binding of lesion DNA and loss of DNA repair. The mutant PhrBI51W , is characterized by the loss of the DMRL chromophore, reduced photoreduction and reduced DNA repair capacity...
December 19, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27986991/recombinant-expression-and-characterization-of-a-l-amino-acid-oxidase-from-the-fungus-rhizoctonia-solani
#4
Katharina Hahn, Katrin Neumeister, Andreas Mix, Tilman Kottke, Harald Gröger, Gabriele Fischer von Mollard
L-Amino acid oxidases (L-AAOs) catalyze the oxidative deamination of L-amino acids to the corresponding α-keto acids, ammonia, and hydrogen peroxide. L-AAOs are homodimeric enzymes with FAD as a non-covalently bound cofactor. They are of potential interest for biotechnological applications. However, heterologous expression has not succeeded in producing large quantities of active recombinant L-AAOs with a broad substrate spectrum so far. Here, we report the heterologous expression of an active L-AAO from the fungus Rhizoctonia solani in Escherichia coli as a fusion protein with maltose-binding protein (MBP) as a solubility tag...
December 16, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27976856/unveiling-the-pathogenic-molecular-mechanisms-of-the-most-common-variant-p-k329e-in-medium-chain-acyl-coa-dehydrogenase-deficiency-by-in-vitro-and-in-silico-approaches
#5
Cátia A Bonito, Joana Nunes, João Leandro, Filipa Louro, Paula Leandro, Fátima V Ventura, Rita C Guedes
Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is the most common genetic disorder affecting the mitochondrial fatty acid β-oxidation pathway. The mature and functional form of human MCAD (hMCAD) is a homotetramer assembled as a dimer of dimers (monomers A/B and C/D). Each monomer binds a FAD cofactor, necessary for the enzyme's activity. The most frequent mutation in MCADD results from the substitution of a lysine with a glutamate in position 304 of mature hMCAD (p.K329E in the precursor protein)...
December 27, 2016: Biochemistry
https://www.readbyqxmd.com/read/27935052/an-ethenoadenine-fad-analog-accelerates-uv-dimer-repair-by-dna-photolyase
#6
Madhavan Narayanan, Vijay R Singh, Goutham Kodali, Kimberly Jacoby, Katarina Moravcevic, Robert J Stanley
Reduced anionic flavin adenine dinucleotide (FADH-) is the critical cofactor in DNA photolyase (PL) for the repair of cyclobutane pyrimidine dimers (CPD) in UV-damaged DNA. The initial step involves photoinduced electron transfer from *FADH- to the CPD. The adenine (Ade) moiety is nearly stacked with the flavin ring, an unusual conformation compared to other FAD-dependent proteins. The role of this proximity has not been unequivocally elucidated. Some studies suggest that Ade is a radical intermediate, but others conclude that Ade modulates the electron transfer rate constant (kET) through superexchange...
December 9, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27923678/flavin-nucleotides-act-as-electron-shuttles-mediating-reduction-of-the-2fe-2s-clusters-in-mitochondrial-outer-membrane-protein-mitoneet
#7
Aaron P Landry, Yiming Wang, Zishuo Cheng, Robert B Crochet, Yong-Hwan Lee, Huangen Ding
MitoNEET, a primary target of type II diabetes drug pioglitazone, has an essential role in regulating energy metabolism, iron homeostasis, and production of reactive oxygen species in mitochondria. Structurally, mitoNEET is anchored to the mitochondrial outer membrane via its N-terminal transmembrane α-helix. The C-terminal cytosolic domain of mitoNEET hosts a redox active [2Fe-2S] cluster via three cysteine and one histidine residues. Here we report that the reduced flavin nucleotides can rapidly reduce the mitoNEET [2Fe-2S] clusters under anaerobic or aerobic conditions...
January 2017: Free Radical Biology & Medicine
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
#8
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
#9
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 the 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...
February 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27845672/gpu-based-point-cloud-superpositioning-for-structural-comparisons-of-protein-binding-sites
#10
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
#11
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
#12
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
#13
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
#14
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...
December 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
#15
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
#16
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
#17
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...
February 2017: 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
#18
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
#19
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
#20
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
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