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Biochemistry

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https://www.readbyqxmd.com/read/28820590/conformational-heterogeneity-in-a-fully-complementary-dna-three-way-junction-with-a-gc-rich-branchpoint
#1
Anita Toulmin, Laura E Baltierra-Jasso, Michael J Morten, Tara Sabir, Peter McGlynn, Gunnar F Schröder, Brian O Smith, Steven W Magennis
DNA three-way junctions (3WJs) are branched structures that serve as important biological intermediates and as components in DNA nanostructures. We recently derived the global structure of a fully-complementary 3WJ and found that it contained unpaired bases at the branchpoint, in support of previous observations of branch flexibility and branchpoint reactivity. By combining high-resolution single-molecule FRET, molecular modeling, time-resolved ensemble fluorescence spectroscopy and the first 19F NMR observations of fully complementary 3WJs, we now show that the 3WJ structure can adopt multiple distinct conformations depending upon the sequence at the branchpoint...
August 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28820582/pathogenic-mutations-induce-partial-structural-changes-in-native-%C3%AE-sheet-structure-of-transthyretin-and-accelerate-aggregation
#2
Kwang Hun Lim, Anvesh K R Dasari, Renze Ma, Ivan Hung, Zhehong Gan, Jeffery W Kelly, Michael C Fitzgerald
Amyloid formation of natively folded proteins involves global and/or local unfolding of the native state to form aggregation-prone intermediates. Here we report solid-state NMR structural studies of amyloid derived from wild-type (WT) and more aggressive mutant forms of transthyretin (TTR) to investigate the structural changes associated with effective TTR aggregation. We employed selective 13C-labeling schemes to investigate structural features of β-structured core regions in amyloid states of WT and two mutant forms (V30M and L55P) of TTR...
August 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28820243/interpreting-reverse-transcriptase-termination-and-mutation-events-for-greater-insight-into-the-chemical-probing-of-rna
#3
Alec N Sexton, Peter Y Wang, Michael Rutenberg-Schoenberg, Matthew D Simon
Chemical probing has the power to provide insight into RNA conformation in vivo and in vitro, but interpreting the results depends on methods to detect the chemically modified nucleotides. Traditionally, the presence of modified bases was inferred from their ability to halt reverse transcriptase during primer extension and the locations of termination sites observed by electrophoresis or sequencing. More recently, modification-induced mutations have been used as a readout for chemical probing data. Given the variable propensity for mismatch incorporation and read-through with different reverse transcriptases, we examined how termination and mutation events compare to each other in the same chemical probing experiments...
August 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28820240/the-interaction-between-the-third-type-iii-domain-from-fibronectin-and-anastellin-involves-%C3%AE-strand-exchange
#4
Jessica M Stine, Gabriel J H Ahl, Casey Schlenker, Domnita-Valeria Rusnac, Klára Briknarová
Anastellin is a small recombinant fragment derived from the extracellular matrix protein fibronectin; it comprises the first type III (FN3) domain without the two N-terminal β-strands. It inhibits angiogenesis, tumor growth, and metastasis in mouse models and requires endogenous fibronectin for its in vivo anti-angiogenic activity. It binds to fibronectin in vitro and converts the soluble protein to insoluble fibrils that structurally and functionally resemble fibronectin fibrils deposited in the extracellular matrix by cells...
August 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28809541/ubiquitin-chains-modified-by-the-bacterial-ligase-sdea-are-protected-from-deubiquitinase-hydrolysis
#5
Kedar Puvar, Yiyang Zhou, Jiazhang Qiu, Zhao-Qing Luo, Mary J Wirth, Chittaranjan Das
The SidE family of Legionella pneumophila effectors is a unique group of ubiquitin-modifying enzymes. Along with catalyzing NAD(+)-dependent ubiquitination of certain host proteins independent of the canonical E1/E2/E3 pathway, they have also been shown to produce phosphoribosylated free ubiquitin. This modified ubiquitin product is incompatible with conventional E1/E2/E3 ubiquitination processes, with the potential to lock down various cellular functions that are dependent on ubiquitin signaling. Here, we show that in addition to free ubiquitin, Lys63-, Lys48-, Lys11-, and Met1-linked diubiquitin chains are also modified by SdeA in a similar fashion...
August 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28816437/selective-targeting-by-a-mechanism-based-inactivator-against-plp-dependent-enzymes-mechanisms-of-inactivation-and-alternative-turnover
#6
Romila Mascarenhas, Hoang V Le, Kenneth D Clevenger, Helaina J Lehrer, Dagmar Ringe, Neil L Kelleher, Richard B Silverman, Dali Liu
Potent mechanism-based inactivators can be rationally designed against PLP-dependent drug targets, such as ornithine aminotransferase (OAT) or γ-aminobutyric acid aminotransferase (GABA-AT). An important challenge, however, is the lack of selectivity towards other PLP-dependent off-target enzymes, because of similarities in mechanisms of all PLP-dependent aminotransferase reactions. On the basis of complex crystal structures, we investigate the inactivation mechanism of OAT, a hepatocellular carcinoma (HCC) target, by (1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP), a known inactivator of GABA-AT...
August 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28762729/activation-and-loading-of-the-starter-unit-during-thiocoraline-biosynthesis
#7
Shogo Mori, Sanjib K Shrestha, Javier Fernández, María Álvarez San Millán, Atefeh Garzan, Ahmad H Al-Mestarihi, Felipe Lombó, Sylvie Garneau-Tsodikova
The initiation of the nonribosomal peptide synthetase (NRPS) assembly of the bisintercalator natural product thiocoraline involves key enzymatic steps for AMP activation and carrier protein loading of the starter unit 3-hydroxyquinaldic acid (3HQA). Gene cluster data combined with protein sequence homology analysis originally led us to propose that TioJ could be responsible for the AMP activation step, whereas TioO could act as the thiolation (T) domain, facilitating the transfer of 3HQA to the next NRPS module, TioR...
August 17, 2017: Biochemistry
https://www.readbyqxmd.com/read/28813589/regulation-of-stability-on-histone-h2a-h2b-dimer-by-h2a-tyr57-phosphorylation
#8
Takuma Sueoka, Gosuke Hayashi, Akimitsu Okamoto
Histone H2A and H2B form a H2A-H2B heterodimer, which is a fundamental unit of nucleosome assembly and disassembly. Several posttranslational modifications change the interface between the H2A-H2B dimer and the H3-H4 tetramer, and regulate nucleosome stability. However, posttranslational modifications associated with the interface between H2A and H2B have not been discussed. In this paper, it is shown that Tyr57 phosphorylation in H2A strongly influences H2A-H2B dimerization. Tyr57-phosphorylated H2A was chemically synthesized and utilized to reconstitute the H2A-H2B dimer and nucleosome as well as canonical H2A...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28813137/site-a-mediated-partial-unfolding-of-cytochrome-c-on-cardiolipin-vesicles-is-species-dependent-and-does-not-require-lys72
#9
Margaret M Elmer-Dixon, Bruce E Bowler
Measurements at pH 8 allow evaluation of binding of 100% cardiolipin vesicles to site A of cytochrome c without interference from other known binding sites. Site A encompasses Lys72, Lys73, Lys86 and Lys87, located in or adjacent to Ω-loop D (residues 70-85), which positions Met80 for binding to the heme. Binding of cytochrome c to cardiolipin disrupts Met80 heme binding, permitting peroxidase activity. Cardiolipin binding to yeast iso-1-cytochrome c versus human cytochrome c is compared to assess how cardiolipin binding to site A has evolved for cytochrome c from species that do not have a complete intrinsic apoptotic pathway to species that do...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28812882/aberrantly-large-single-channel-conductance-of-polyhistidine-arm-containing-protein-nanopores
#10
Avinash Kumar Thakur, Motahareh Ghahari Larimi, Kristin Gooden, Liviu Movileanu
There have been only a few studies reporting on the impact of polyhistidine affinity tags on the structure, function, and dynamics of proteins. Because of their relatively short size, they are often assumed to have little or no effect on the conformation and activity of a protein. Here, using membrane protein design and single-molecule electrophysiology, we determined that the presence of a hexahistidine arm at the N-terminus of a truncated FhuA-based protein nanopore, leaving the C-terminus untagged, produces an unusual increase in the unitary conductance up to ~8 nS in 1 M KCl...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28767234/effects-of-catalytic-action-and-ligand-binding-on-conformational-ensembles-of-adenylate-kinase
#11
Emre Onuk, John Badger, Yu Jing Wang, Jaydeep Bardhan, Yasmin Chishti, Murat Akcakaya, Dana H Brooks, Deniz Erdogmus, David D L Minh, Lee Makowski
Crystal structures of adenylate kinase (AdK) from Escherichia coli capture two states: an "open" conformation (apo) obtained in the absence of ligands and a "closed" conformation in which ligands are bound. Other AdK crystal structures suggest intermediate conformations that may lie on the transition pathway between these two states. To characterize the transition from open to closed states in solution, X-ray solution scattering data were collected from AdK in the apo form and with progressively increasing concentrations of five different ligands...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28766335/functional-complementation-studies-reveal-different-interaction-partners-of-escherichia-coli-iscs-and-human-nfs1
#12
Martin Bühning, Martin Friemel, Silke Leimkühler
The trafficking and delivery of sulfur to cofactors and nucleosides is a highly regulated and conserved process among all organisms. All sulfur transfer pathways generally have an l-cysteine desulfurase as an initial sulfur-mobilizing enzyme in common, which serves as a sulfur donor for the biosynthesis of sulfur-containing biomolecules like iron-sulfur (Fe-S) clusters, thiamine, biotin, lipoic acid, the molybdenum cofactor (Moco), and thiolated nucleosides in tRNA. The human l-cysteine desulfurase NFS1 and the Escherichia coli homologue IscS share a level of amino acid sequence identity of ∼60%...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28762722/posttranslational-modification-of-heme-b-in-a-bacterial-peroxidase-the-role-of-heme-to-protein-ester-bonds-in-ligand-binding-and-catalysis
#13
Andrea Nicolussi, Markus Auer, Julia Weissensteiner, Georg Schütz, Sonja Katz, Daniel Maresch, Stefan Hofbauer, Marzia Bellei, Gianantonio Battistuzzi, Paul G Furtmüller, Christian Obinger
The existence of covalent heme to protein bonds is the most striking structural feature of mammalian peroxidases, including myeloperoxidase and lactoperoxidase (LPO). These autocatalytic posttranslational modifications (PTMs) were shown to strongly influence the biophysical and biochemical properties of these oxidoreductases. Recently, we reported the occurrence of stable LPO-like counterparts with two heme to protein ester linkages in bacteria. This study focuses on the model wild-type peroxidase from the cyanobacterium Lyngbya sp...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28758387/characterization-of-heme-orientational-disorder-in-a-myoglobin-reconstituted-with-a-trifluoromethyl-group-substituted-heme-cofactor
#14
Yuki Kanai, Ayaka Harada, Tomokazu Shibata, Ryu Nishimura, Kosuke Namiki, Miho Watanabe, Shunpei Nakamura, Fumiaki Yumoto, Toshiya Senda, Akihiro Suzuki, Saburo Neya, Yasuhiko Yamamoto
The orientation of a CF3-substituted heme in sperm whale myoglobin and L29F, H64L, L29F/H64Q, and H64Q variant proteins has been investigated using (19)F NMR spectroscopy to elucidate structural factors responsible for the thermodynamic stability of the heme orientational disorder, i.e., the presence of two heme orientations differing by a 180° rotation about the 5-15 meso axis, with respect to the protein moiety. Crystal structure of the met-aquo form of the wild-type myoglobin reconstituted with 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7-trifluoromethylporphyrinatoiron(III), determined at resolution of 1...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28749131/lysine-deacetylases-exhibit-distinct-changes-in-activity-profiles-due-to-fluorophore-conjugation-of-substrates
#15
Tasha B Toro, Jenae R Bryant, Terry J Watt
Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Thousands of potential substrates, acetylated protein sequences, have been identified in mammalian cells. Properly regulated acetylation and deacetylation have been linked to many biological processes, while aberrant KDAC activity has also been linked to numerous diseases. Commercially available peptide substrates that are conjugated to fluorescent dye molecules, such as 7-amino-4-methylcoumarin (AMC), are commonly used to monitor deacetylation in studies addressing both substrate specificity and small molecule modulators of activity...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28726391/tumor-associated-mutations-in-caspase-6-negatively-impact-catalytic-efficiency
#16
Kevin B Dagbay, Maureen E Hill, Elizabeth Barrett, Jeanne A Hardy
Unregulated, particularly suppressed programmed cell death is one of the distinguishing features of many cancer cells. The cysteine protease caspase-6, one of the executioners of apoptotic cell death, plays a crucial role in regulation of apoptosis. Several somatic mutations in the CASP6 gene in tumor tissues have been reported. This work explores the effect of CASP6 tumor-associated mutations on the catalytic efficiency and structure of caspase-6. In general, these mutations showed decreased overall rates of catalytic turnover...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28809557/in-silico-and-in-vitro-interactions-between-short-chain-fatty-acids-and-human-histone-deacetylases
#17
Rou Hui Ho, James Chun Yip Chan, Hao Fan, Dorinda Yan Qin Kioh, Bee Wah Lee, Eric Chun Yong Chan
Short chain fatty acids (SCFAs) are postulated to modulate the immune development of neonates via epigenetic regulations such as histone deacetylase (HDAC) inhibition. In the context of atopic diseases, the inhibition of HDAC maintains T-cell homeostasis and induces naïve T-cell differentiation into adaptive Treg, which regulates the production of anti-inflammatory cytokines and suppression of Th2 immune responses. We investigated the structure-inhibition relationships of SCFAs with class I HDAC3 and class IIa HDAC7 using in silico docking simulation and in vitro human recombinant HDAC inhibition assay...
August 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28809546/staphylococcus-aureus-cidc-is-a-pyruvate-menaquinone-oxidoreductase
#18
Xinyan Zhang, Kenneth W Bayles, Sorin Luca
Recent studies have revealed an important role for the Staphylococcus aureus CidC enzyme in cell death during the stationary phase and in biofilm development, and have contributed to our understanding of the metabolic processes important in the induction of bacterial programmed cell death (PCD). To gain more insight into the characteristics of this enzyme, we performed an in-depth biochemical and biophysical analysis of its catalytic properties. In vitro experiments show that this flavoprotein catalyzes the oxidative decarboxylation of pyruvate to acetate and carbon dioxide...
August 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28809494/on-protein-assembly-and-building-blocks-beyond-the-limits-of-the-lego-bricks-metaphor
#19
Yaakov Levy
Proteins, similarly to other biomolecules, have a modular and hierarchical structure. Various building blocks serve to construct proteins of high structural complexity and diverse functionality. In multi-domain proteins, for example, domains are fused to each other in different combinations to achieve different functions. Although the LEGO bricks metaphor is justified as a means of simplifying the complexity of 3-dimensional protein structures, several fundamental properties (such as allostery or the induced-fit mechanism) make deviation from it necessary to respect the plasticity, softness, and cross-talks that are essential to protein function...
August 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28809482/structural-dynamics-of-15-lipoxygenase-2-via-hydrogen-deuterium-exchange
#20
Kristin Diane Droege, Mary E Keithly, Charles R Sanders, Richard N Armstrong, Matthew K Thompson
Eicosanoids are inflammatory signaling lipids that are biosynthesized in response to cellular injury or threat. They were originally thought to be pro-inflammatory molecules, but at least one sub-class, the lipoxins, are able to resolve inflammation. The first step in lipoxin synthesis is the oxygenation of arachidonic acid by 15-Lipoxygenase (15-LOX). 15-LOX contains two domains: a Ca2+ binding PLAT domain and a catalytic domain. 15-LOX is a soluble cytosolic protein until Ca2+ binding to the PLAT domain promotes translocation to the membrane surface...
August 15, 2017: Biochemistry
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