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Biochemistry

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https://www.readbyqxmd.com/read/28650656/cytotoxic-and-mutagenic-properties-of-c3-epimeric-lesions-of-2-deoxyribonucleosides-in-escherichia-coli-cells
#1
Pengcheng Wang, Nicholas J Amato, Yinsheng Wang
Reactive oxygen species (ROS), resulting from endogenous metabolism and/or environmental exposure, can induce damage to the 2-deoxyribose moiety in DNA. Specifically, a hydrogen atom from each of the five carbon atoms in 2-deoxyribose can be abstracted by hydroxyl radical, and improper chemical repair of the ensuing radicals formed at the C1', C3', and C4' positions can lead to the stereochemical inversion at these carbons to yield epimeric 2-deoxyribose lesions. Although single-nucleobase lesions induced by ROS have been well characterized, few studies have been conducted to examine the biological consequences of the C3'-epimeric lesions of 2'-deoxynucleosides, i...
June 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28650145/the-dead-box-protein-cyt-19-uses-arginine-residues-in-its-c-tail-to-tether-rna-substrates
#2
Veronica F Busa, Maxwell J Rector, Rick Russell
DEAD-box proteins are nonprocessive RNA helicases that play diverse roles in cellular processes. The Neurospora crassa DEAD-box protein CYT-19 promotes mitochondrial group I intron splicing and functions as a general RNA chaperone. CYT-19 includes a disordered, arginine-rich 'C-tail' that binds RNA, positioning the helicase core to capture and unwind nearby RNA helices. Here we probed the C-tail further by varying the number and positions of arginines within it. We found that removing sets of as few as four of the eleven arginines reduced RNA unwinding activity (kcat/KM) equivalently to removing the C-tail, suggesting that a minimum or 'threshold' number of arginines is required...
June 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28649833/functional-prioritization-and-hydrogel-regulation-phenomena-created-by-a-combinatorial-pearl-associated-2-protein-biomineralization-model-system
#3
Gaurav Jain, Martin Pendola, Yu-Chieh Huang, Denis Gebauer, José Juan-Colás, Steven D Johnson, John Spencer Evans
In the nacre or aragonitic layer of the oyster pearl there exists a 12-member proteome which regulates both the early stages of nucleation and nano-to-mesoscale assembly of nacre tablets and calcitic crystals from mineral nanoparticle precursors. Several approaches have been developed to understand protein-associated mechanisms of pearl nacre formation, yet we still lack insight into how protein ensembles or proteomes manage nucleation and crystal growth. To provide additional insights we have created a proportionally-defined combinatorial model consisting of two pearl nacre-associated proteins, PFMG1 and PFMG2 (shell oyster pearl nacre, P...
June 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28617588/biosynthesis-of-single-thioether-c-type-cytochromes-provides-insight-into-mechanisms-intrinsic-to-holocytochrome-c-synthase-hccs
#4
Shalon E Babbitt, Jennifer Hsu, Deanna L Mendez, Robert G Kranz
C-type cytochromes (cyts c) are generally characterized by the presence of two thioether attachments between heme and two cysteine residues within a highly conserved CXXCH motif. Most eukaryotes use the System III cyt c biogenesis pathway composed of holocytochrome c synthase (HCCS) to catalyze thioether formation. Some protozoan organisms express a functionally equivalent, natural variant of cyt c with an XXXCH heme-attachment motif, resulting in a single covalent attachment. Previous studies have shown that recombinant HCCS can produce low levels of the XXXCH single thioether variant...
June 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28616989/reconstructed-serine-288-in-the-left-flipper-region-of-the-rat-p2x7-receptor-stabilizes-nonsensitized-states
#5
Yevheniia Ishchenko, Nataliia Novosolova, Kamil Khafizov, Geneviève Bart, Arina Timonina, Dmitriy Fayuk, Andrei Skorinkin, Rashid Giniatullin
Serine 275, a conserved residue of the left flipper region of ATP-gated P2X3 receptors, plays a key role in both agonist binding and receptor desensitization. It is conserved in most of the P2X receptors except P2X7 and P2X6. By combining experimental patch-clamp and modeling approaches, we explored the role of the corresponding residue in the rat P2X7 receptor (rP2X7) by replacing the phenylalanine at position 288 with serine and characterizing the membrane currents generated by either the wild-type (WT) or the mutated rP2X7 receptor...
June 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28616972/dss1-regulates-association-of-brh2-with-rad51
#6
Qingwen Zhou, William K Holloman
Brh2, the BRCA2 ortholog in the fungus Ustilago maydis, mediates delivery of Rad51 to DNA during the course of homology-directed DNA repair. Rad51 interacts with Brh2 through the highly conserved BRC element and through a second region termed CRE located at the extreme carboxy terminus. Dss1, a small intrinsically unstructured protein that interacts with Brh2, is crucial for its activity in DNA repair, but the mechanism of this regulation is uncertain. In previous studies, we found that interaction of Brh2 with DNA was strongly modulated by association with Dss1...
June 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28614667/n-glycosylation-of-asparagine-130-in-the-extracellular-domain-of-the-human-calcitonin-receptor-significantly-increases-peptide-hormone-affinity
#7
Sang-Min Lee, Jason M Booe, Joseph J Gingell, Virginie Sjoelund, Debbie L Hay, Augen A Pioszak
The calcitonin receptor (CTR) is a class B G protein-coupled receptor that is activated by the peptide hormones calcitonin and amylin. Calcitonin regulates bone remodeling through CTR, whereas amylin regulates blood glucose and food intake by activating CTR in complex with receptor activity-modifying proteins (RAMPs). These receptors are targeted clinically for the treatment of osteoporosis and diabetes. Here, we define the role of CTR N-glycosylation in hormone binding using purified calcitonin and amylin receptor extracellular domain (ECD) glycoforms and fluorescence polarization/anisotropy and isothermal titration calorimetry peptide-binding assays...
June 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28603981/the-enigmatic-p450-decarboxylase-olet-is-capable-of-but-evolved-to-frustrate-oxygen-rebound-chemistry
#8
Chun H Hsieh, Xiongyi Huang, José A Amaya, Cooper D Rutland, Carson L Keys, John T Groves, Rachel N Austin, Thomas M Makris
OleT is a cytochrome P450 enzyme that catalyzes the removal of carbon dioxide from variable chain length fatty acids to form 1-alkenes. In this work, we examine the binding and metabolic profile of OleT with shorter chain length (n ≤ 12) fatty acids that can form liquid transportation fuels. Transient kinetics and product analyses confirm that OleT capably activates hydrogen peroxide with shorter substrates to form the high-valent intermediate Compound I and largely performs C-C bond scission. However, the enzyme also produces fatty alcohol side products using the high-valent iron oxo chemistry commonly associated with insertion of oxygen into hydrocarbons...
June 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28644006/structure-of-the-forkhead-domain-of-foxa2-bound-to-a-complete-dna-consensus-site
#9
Jun Li, Ana Carolina Dantas Machado, Ming Guo, Jared M Sagendorf, Zhan Zhou, Longying Jiang, Xiaojuan Chen, Daichao Wu, Lingzhi Qu, Zhu-Chu Chen, Lin Chen, Remo Rohs, Yongheng Chen
FOXA2, a member of the forkhead family of transcription factors, plays essential roles in liver development and bile acid homeostasis. In this study, we report a 2.8 Å co-crystal structure of the FOXA2 DNA-binding domain (FOXA2-DBD) bound to a DNA duplex containing a forkhead consensus binding site (GTAAACA). FOXA2-DBD adopts the canonical winged-helix fold, with helix H3 and wing 1 regions mainly mediating the DNA recognition. Although the wing 2 region was not defined in the structure, isothermal titration calorimetry (ITC) assays suggested that this region was required for optimal DNA binding...
June 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28644004/the-intricate-effects-of-alpha-amino-and-lysine-modifications-on-arginine-methylation-on-the-n-terminal-tail-of-histone-h4
#10
Melody D Fulton, Jing Zhang, Maomao He, Meng-Chiao Ho, Y George Zheng
Chemical modifications on the DNA and nucleosomal histones tightly control the gene transcription program in eukaryotic cells. The "histone code" hypothesis proposes that the frequency, combination, and location of post-translational modifications (PTMs) on the core histones compose a complex network of epigenetic regulation. Currently, there are at least 23 different types and over 450 histone PTMs discovered, and the PTMs on lysine and arginine residues account for a crucial part of the histone code. Although significant progress has been achieved in recent years, the molecular basis for the histone code is far from being fully understood...
June 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28640638/enzyme-mediated-conversion-of-fad-to-8-formyl-fad-in-formate-oxidase-results-in-modified-cofactor-with-enhanced-catalytic-properties
#11
John M Robbins, Michael G Souffrant, Donald Hamelberg, Giovanni Gadda, Andreas S Bommarius
Flavins, including flavin adenine dinucleotide (FAD), are fundamental catalytic cofactors responsible for the redox functionality of a diverse set of proteins. Alternatively, modified flavin analogues are rarely found in nature as their incorporation typically results in inactivation of flavoproteins, thus leading to the disruption of important cellular pathways. Here, we report that the fungal flavoenzyme formate oxidase (FOX) catalyzes the slow conversion of non-covalently bound FAD to 8-formyl FAD (8-fFAD), and that this conversion results in a nearly 10-fold increase in formate oxidase activity...
June 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28640600/horse-liver-alcohol-dehydrogenase-zinc-coordination-and-catalysis
#12
Bryce V Plapp, Baskar Raj Savarimuthu, Daniel J Ferraro, Jon K Rubach, Eric N Brown, Subramanian Ramaswamy
: During catalysis by liver alcohol dehydrogenase (ADH), a water bound to the catalytic zinc is replaced by the oxygen of the substrates. The mechanism may involve a pentacoordinated zinc or a double displacement reaction with participation by a nearby glutamate residue, as suggested by studies of human ADH3, yeast ADH1 and some other tetrameric ADHs. Zinc coordination and participation of water in the enzyme mechanism were investigated by X-ray crystallography. Apoenzyme and its complex with adenosine 5'-diphosphoribose have an open protein conformation with the catalytic zinc in one position, tetracoordinated by Cys-46, His-67, Cys-174 and a water molecule...
June 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28640592/identification-of-a-small-molecule-activator-for-aphb-a-lysr-type-virulence-transcriptional-regulator-in-vibrio-cholerae
#13
Britney Privett, Maria Pellegrini, Gabriela Kovacikova, Ronald Taylor, Karen Skorupski, Dale F Mierke, F Jon Kull
AphB is a LysR-type transcriptional regulator (LTTR) that cooperates with a second transcriptional activator, AphA, at the tcpPH promoter to initiate expression of the virulence cascade in Vibrio cholerae. Since it is not yet known whether AphB responds to a natural ligand in V. cholerae that influences its ability to activate transcription, we used a computational approach to identify small molecules that influence its activity. In silico docking was used to identify potential ligands for AphB, and saturation transfer difference NMR was subsequently employed to access the validity of promising targets...
June 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28640584/spectroscopic-evidence-for-a-h-bond-network-at-y356-located-at-the-subunit-interface-of-active-e-coli-ribonucleotide-reductase
#14
Thomas U Nick, Kanchana R Ravichandran, JoAnne Stubbe, Müge Kasanmascheff, Marina Bennati
The reaction catalyzed by E. coli ribonucleotide reductase (RNR) composed of α and β subunits that form an active α2β2 complex is a paradigm for proton-coupled electron transfer (PCET) processes in biological transformations. β2 contains the diferric tyrosyl radical (Y122•) cofactor that initiates a radical transfer (RT) over 35 Å via a specific pathway of amino acids (Y122• ↔ [W48] ↔ Y356 in β2 to Y731 ↔Y730↔ C439 in α2). Experimental evidence exists for co-linear and orthogonal PCET in α2 and β2 respectively...
June 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28562023/mechanistic-insight-from-calorimetric-measurements-of-the-assembly-of-the-binuclear-metal-active-site-of-glycerophosphodiesterase-gpdq-from-enterobacter-aerogenes
#15
Marcelo M Pedroso, Fernanda Ely, Margaret C Carpenter, Nataša Mitić, Lawrence R Gahan, David L Ollis, Dean E Wilcox, Gerhard Schenk
Glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a binuclear metallohydrolase with a high affinity for metal ions at its α site but a lower affinity at its β site in the absence of a substrate. Isothermal titration calorimetry (ITC) has been used to quantify the Co(II) and Mn(II) binding affinities and thermodynamics of the two sites in wild-type GpdQ and two mutants, both in the absence and in the presence of phosphate. Metal ions bind to the six-coordinate α site in an entropically driven process with loss of a proton, while binding at the β site is not detected by ITC...
June 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28636371/iron-oxidation-and-core-formation-in-recombinant-heteropolymeric-human-ferritins
#16
Matthew R Mehlenbacher, Maura Poli, Paolo Arosio, Paolo Santambrogio, Sonia Levi, N Dennis Chasteen, Fadi Bou-Abdallah
In animals, the iron storage and detoxification protein, ferritin, is composed of two functionally and genetically distinct subunit types, H (Heavy) and L (Light), which co-assemble in various ratios with tissue specific distributions to form shell-like protein structures of 24 subunits within which a mineralized iron core is stored. The H-subunit possesses a ferroxidase center (FC) which catalyzes Fe(II) oxidation whereas the L-subunit does not. To assess the role of the L-subunit in iron oxidation and core formation, two human recombinant heteropolymeric ferritins, designated H-rich and L-rich with ratios of ~ 20H:4L and ~ 22L:2H, respectively, were employed and compared to the human homopolymeric H-subunit ferritin (HuHF)...
June 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28636341/biochemical-characterization-of-wbkc-an-n-formyltransferase-from-brucella-melitensis
#17
Alexander S Riegert, Daniel P Chantigian, James B Thoden, Peter A Tipton, Hazel M Holden
It has become increasingly apparent within the last several years that unusual N-formylated sugars are often found on the O-antigens of such Gram negative pathogenic organisms as Francisella tularensis, Campylobacter jejuni, and Providencia alcalifaciens, amongst others. Indeed, in some species of Brucella, for example, the O-antigen contains 1,2-linked 4-formamido-4,6-dideoxy-alpha-D-mannosyl groups. These sugars, often referred to as N-formylperosamine, are synthesized in pathways initiating with GDP-mannose...
June 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28635262/enormous-hydrogen-bond-strength-enhancement-through-%C3%AF-conjugation-gain-implications-for-enzyme-catalysis
#18
Chia-Hua Wu, Keigo Ito, Allyson Buytendyk, Kit Hansell Bowen, Judy I Wu
Surprisingly large "resonance-assistance" effects may explain how some enzymes form extremely short, strong hydrogen bonds to stabilize reactive oxyanion intermediates and facilitate catalysis. Computational models for several enzymic residue-substrate interactions reveal that when a π-conjugated, proton donor (XH) forms a hydrogen bond to a charged substrate (Y-), XH can become significantly more π-electron delocalized, and this "extra" stabilization may boost the [XH…Y-] hydrogen bond strength by up to 15 kcal/mol...
June 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28603979/clinically-divergent-mutation-effects-on-the-structure-and-function-of-the-human-cardiac-tropomyosin-overlap
#19
Mark McConnell, Lauren Tal Grinspan, Michael R Williams, Melissa L Lynn, Benjamin A Schwartz, Ofer Z Fass, Steven D Schwartz, Jil C Tardiff
The progression of genetically inherited cardiomyopathies from an altered protein structure to clinical presentation of disease is not well understood. One of the main roadblocks to mechanistic insight remains a lack of high-resolution structural information about multiprotein complexes within the cardiac sarcomere. One example is the tropomyosin (Tm) overlap region of the thin filament that is crucial for the function of the cardiac sarcomere. To address this central question, we devised coupled experimental and computational modalities to characterize the baseline function and structure of the Tm overlap, as well as the effects of mutations causing divergent patterns of ventricular remodeling on both structure and function...
June 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28598148/effect-of-a-k72a-mutation-on-the-structure-stability-dynamics-and-peroxidase-activity-of-human-cytochrome-c
#20
Shiloh M Nold, Haotian Lei, Tung-Chung Mou, Bruce E Bowler
We test the hypothesis that Lys72 suppresses the intrinsic peroxidase activity of human cytochrome c, as observed previously for yeast iso-1-cytochrome c [McClelland, L. J., et al. (2014) Proc. Natl. Acad. Sci. U. S. A. 111, 6648-6653]. A 1.25 Å X-ray structure of K72A human cytochrome c shows that the mutation minimally affects structure. Guanidine hydrochloride denaturation demonstrates that the K72A mutation increases global stability by 0.5 kcal/mol. The K72A mutation also increases the apparent pKa of the alkaline transition, a measure of the stability of the heme crevice, by 0...
June 21, 2017: Biochemistry
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