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Archives of Biochemistry and Biophysics

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https://www.readbyqxmd.com/read/28428039/antimicrobial-mechanism-of-epigallocatechin-gallate-and-gallocatechin-gallate-they-target-1-deoxy-d-xylulose-5-phosphate-reductoisomerase-the-key-enzyme-of-the-mep-terpenoid-biosynthetic-pathway
#1
Xian Hui, Shui-Hong Hua, Qian-Qian Wu, Heng Li, Wen-Yun Gao
The catechins EGCG and GCG show a variety of pharmacological activities, especially an antibacterial capacity, but their modes of antimicrobial action have not been fully elucidated. 1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), the first key enzyme in the MEP pathway for terpenoid biosynthesis, is a recently validated antimicrobial target. In order to disclose the antibacterial mechanism of EGCG and GCG, the DXR inhibitory activity of them was investigated in this study. The data show that EGCG and GCG both could specifically suppress the activity of DXR, with EGCG exhibiting relatively low effect against DXR (IC50 about 210 μM) and GCG displaying strong activity (IC50 27...
April 18, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28412156/tyrosine-oxidation-and-nitration-in-transmembrane-peptides-is-connected-to-lipid-peroxidation
#2
Silvina Bartesaghminni, Daniel Herrera, Débora M Martinez, Ariel Petruk, Verónica Demicheli, Madia Trujillo, Marcelo A Martí, Darío A Estrín, Rafael Radi
Tyrosine nitration is an oxidative post-translational modification that can occur in proteins associated to hydrophobic bio-structures such as membranes and lipoproteins. In this work, we have studied tyrosine nitration in membranes using a model system consisting of phosphatidylcholine liposomes with pre-incorporated tyrosine-containing 23 amino acid transmembrane peptides. Tyrosine residues were located at positions 4, 8 or 12 of the amino terminal, resulting in different depths in the bilayer. Tyrosine nitration was accomplished by exposure to peroxynitrite and a peroxyl radical donor or hemin in the presence of nitrite...
April 13, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28341248/abnormal-lipid-lipoprotein-metabolism-and-high-plasma-testosterone-levels-in-male-but-not-female-aromatase-knockout-mice
#3
Akiko Amano, Yoshitaka Kondo, Yoshihiro Noda, Mitsuhiro Ohta, Noriaki Kawanishi, Shuichi Machida, Kazuteru Mitsuhashi, Takafumi Senmaru, Michiaki Fukui, Osamu Takaoka, Taisuke Mori, Jo Kitawaki, Masafumi Ono, Toshiji Saibara, Hiroshi Obayashi, Akihito Ishigami
Sex steroid hormones, such as estrogen and testosterone, are believed to play important roles in lipid metabolism. To elucidate the effects of estrogen depletion on lipid metabolism in male and female mice, we used aromatase-knockout (ArKO) mice, in which Cyp19 gene disruption prevented estrogen synthesis in vivo. These mice were divided into the following 4 groups: male and female ArKO mice and male and female wild-type (WT) mice. These mice were fed a normal-fat diet (13.6% fat) ad libitum. At 159 days after birth, the mice were tested for liver and plasma lipid content and hepatic hormone receptor- and lipid/lipoprotein metabolism-related gene expression...
March 22, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28263718/nmr-based-automated-protein-structure-determination
#4
Julia M Würz, Sina Kazemi, Elena Schmidt, Anurag Bagaria, Peter Güntert
NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures...
March 2, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28263717/nmr-based-stable-isotope-resolved-metabolomics-in-systems-biochemistry
#5
Andrew N Lane, Teresa W-M Fan
Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined...
March 2, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28259514/the-emperor-s-new-clothes-myths-and-truths-of-in-cell-nmr
#6
REVIEW
Annalisa Pastore, Piero Andrea Temussi
In-cell NMR is a technique developed to study the structure and dynamical behavior of biological macromolecules in their natural environment, circumventing all isolation and purification steps. In principle, the potentialities of the technique are enormous, not only for the possibility of bypassing all purification steps but, even more importantly, for the wealth of information that can be gained from directly monitoring interactions among biological macromolecules in a natural cell. Here, we review critically the promises, successes and limits of this technique as it stands now...
March 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28236679/corrigendum-to-conformational-status-of-cytochrome-c-upon-n-homocysteinylation-implications-to-cytochrome-c-release-arch-%C3%A2-biochem-biophys-614-2017-23-27
#7
Gurumayum Suraj Sharma, Laishram Rajendrakumar Singh
No abstract text is available yet for this article.
February 22, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28235467/identification-and-characterization-of-a-novel-starch-branching-enzyme-from-the-picoalgae-ostreococcus-tauri
#8
Nicolas Hedin, Julieta Barchiesi, Diego F Gomez-Casati, Alberto A Iglesias, Miguel A Ballicora, María V Busi
Starch branching enzyme is a highly conserved protein from plants to algae. This enzyme participates in starch granule assembly by the addition of α-1,6-glucan branches to the α-1,4-polyglucans. This modification determines the structure of amylopectin thus arranging the final composition of the starch granule. Herein, we describe the function of the Ot01g03030 gene from the picoalgae Ostreococcus tauri. Although in silico analysis suggested that this gene codes for a starch debranching enzyme, our biochemical studies support that this gene encodes a branching enzyme (BE)...
February 21, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28137423/mechanism-of-inhibition-of-botulinum-neurotoxin-type-a-light-chain-by-two-quinolinol-compounds
#9
Yacoba V T Minnow, Ronald Goldberg, Sreedhar R Tummalapalli, David P Rotella, Nina M Goodey
Quinolinol-based compounds are a promising starting point for discovery of effective inhibitors of the clostridial neurotoxin, botulinum neurotoxin type A light chain (BoNT/A LC). Insights into the mechanism of inhibition by quinolinol compounds facilitate interpretation of docking data and inhibitor optimization. In this study, a fluorogenic substrate of BoNT/A, SNAPtide, was used to study the mechanism by which two new quinolinol compounds, MSU58 and MSU84, with IC50 values of 3.3 μM and 5.8 μM, respectively, inhibit BoNT/A LC...
January 28, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28412155/ascorbic-acid-inhibits-human-insulin-aggregation-and-protects-against-amyloid-induced-cytotoxicity
#10
Parvez Alam, Ayesha Zainab Beg, Mohammad Khursheed Siddiqi, Sumit Kumar Chaturvedi, Ravi Kant Rajpoot, Mohd Rehan Ajmal, Masihuz Zaman, Ali S Abdelhameed, Rizwan Hasan Khan
Protein aggregation into oligomers and fibrils are associated with many human pathophysiologies. Compounds that modulate protein aggregation and interact with preformed fibrils and convert them to less toxic species, expect to serve as promising drug candidates and aid to the drug development efforts against aggregation diseases. In present study, the kinetics of amyloid fibril formation by human insulin (HI) and the anti-amyloidogenic activity of ascorbic acid (AA) were investigated by employing various spectroscopic, imaging and computational approaches...
May 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28396256/structural-insights-into-the-activation-mechanisms-of-human-htra-serine-proteases
#11
REVIEW
Dorota Zurawa-Janicka, Tomasz Wenta, Miroslaw Jarzab, Joanna Skorko-Glonek, Przemyslaw Glaza, Artur Gieldon, Jerzy Ciarkowski, Barbara Lipinska
Human HtrA1-4 proteins belong to the HtrA family of evolutionarily conserved serine proteases and function as important modulators of many physiological processes, including maintenance of mitochondrial homeostasis, cell signaling and apoptosis. Disturbances in their action are linked to severe diseases, including oncogenesis and neurodegeneration. The HtrA1-4 proteins share structural and functional features of other members of the HtrA protein family, however there are several significant differences in structural architecture and mechanisms of action which makes each of them unique...
May 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28392212/n-acetylcysteine-improves-the-quality-of-red-blood-cells-stored-for-transfusion
#12
Florencia Amen, Andrea Machin, Cristina Touriño, Ismael Rodríguez, Ana Denicola, Leonor Thomson
Storage inflicts a series of changes on red blood cells (RBC) that compromise the cell survival and functionality; largely these alterations (storage lesions) are due to oxidative modifications. The possibility of improving the quality of packed RBC stored for transfusion including N-acetylcysteine (NAC) in the preservation solution was explored. Relatively high concentrations of NAC (20-25 mM) were necessary to prevent the progressive leakage of hemoglobin, while lower concentrations (≥2.5 mM) were enough to prevent the loss of reduced glutathione during the first 21 days of storage...
May 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28389299/msrb3-deficiency-induces-cancer-cell-apoptosis-through-p53-independent-and-er-stress-dependent-pathways
#13
Geun-Hee Kwak, Hwa-Young Kim
We have previously shown that down-regulation of methionine sulfoxide reductase B3 (MsrB3) induces cancer cell apoptosis through the activation of the intrinsic mitochondrial pathway. However, the mechanism through which MsrB3 deficiency results in cancer cell death is poorly understood. In this study, we investigated whether p53 and endoplasmic reticulum (ER) stress are involved in MsrB3 deficiency-induced cancer cell apoptosis using breast and colon cancer cells. MsrB3 depletion resulted in p53 down-regulation at the post-transcriptional level...
May 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28389298/stimulatory-and-inhibitory-effects-of-pkc-isozymes-are-mediated-by-serine-threonine-pkc-sites-of-the-cav2-3%C3%AE-1-subunits
#14
Senthilkumar Rajagopal, Brittney K Burton, Blanche L Fields, India O El, Ganesan L Kamatchi
Protein kinase C (PKC) isozymes modulate voltage-gated calcium (Cav) currents through Cav2.2 and Cav2.3 channels by targeting serine/threonine (Ser/Thr) phosphorylation sites of Cavα1 subunits. Stimulatory (Thr-422, Ser-2108 and Ser-2132) and inhibitory (Ser-425) sites were identified in the Cav2.2α1 subunits to PKCs βII and ε. In the current study, we investigated if the homologous sites of Cav2.3α1 subunits (stimulatory: Thr-365, Ser-1995 and Ser-2011; inhibitory: Ser-369) behaved in similar manner. Several Ala and Asp mutants were constructed in Cav2...
May 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28389297/fbxo25-regulates-mapk-signaling-pathway-through-inhibition-of-erk1-2-phosphorylation
#15
Felipe R Teixeira, Adriana O Manfiolli, Nichelle A Vieira, Ana Carla Medeiros, Priscila de O Coelho, Dimitrius Santiago Guimarães, Deborah Schechtman, Marcelo D Gomes
The FBXO25 mediates degradation of ELK-1 and thus inhibits transcriptional activation of immediate early genes (iEG). Here we show that FBXO25 regulates yet another node of this signaling pathway, by decreasing MAPK/ERK activity. We show that induction of FBXO25 reduced ERK1/2 phosphorylation independently of MEK1/2. Accordingly, in HAP1 FBXO25 knockout cells (FBXO25(KO)), we observed that upon PMA treatment ERK1/2 was more active than in parental cells. An increase in cell proliferation under receptor mediated activation of the ERK signaling pathway in FBXO25(KO) cells was also observed...
May 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28288797/overcoming-electrostatic-repulsions-during-amyloid-assembly-effect-of-ph-and-interaction-with-divalent-metals-using-model-peptides
#16
Rodrigo Diaz-Espinoza, Esteban Nova, Octavio Monasterio
Amyloids are polypeptide aggregates involved in many pathologies including Alzheimer's disease. Amyloid assembly is a complex process affected by different interactions including hydrogen bonding, van der Waals forces and electrostatic interactions. The highly regular amyloid structure allows for an arrangement of residues that forces side chains to be closely positioned, giving rise to potentially unfavorable interactions such as electrostatic repulsions. In these cases, amyloid assembly will depend on a balance between stabilizing versus unfavorable interactions...
May 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28359644/thermodynamics-of-tunnel-formation-upon-substrate-binding-in-a-processive-glycoside-hydrolase
#17
Anne Grethe Hamre, Emil Ebbestad Frøberg, Vincent G H Eijsink, Morten Sørlie
Glycoside hydrolases (GHs) catalyze the hydrolysis of glycosidic bonds and are key enzymes in carbohydrate metabolism. Efficient degradation of recalcitrant polysaccharides such as chitin and cellulose is accomplished due to synergistic enzyme cocktails consisting of accessory enzymes and mixtures of GHs with different modes of action and active site topologies. The substrate binding sites of chitinases and cellulases often have surface exposed aromatic amino acids and a tunnel or cleft topology. The active site of the exo-processive chitinase B (ChiB) from Serratia marcescens is partially closed, creating a tunnel-like catalytic cleft...
April 15, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28347661/functional-characterization-of-a-common-cyp4f11-genetic-variant-and-identification-of-functionally-defective-cyp4f11-variants-in-erythromycin-metabolism-and-20-hete-synthesis
#18
Myeongjin Yi, Sun-Ah Cho, Jungki Min, Dong Hyun Kim, Jae-Gook Shin, Su-Jun Lee
CYP4F11, together with CYP4F2, plays an important role in the synthesis of 20-hydroxyeicosatetraenoic acid (20-HETE) from arachidonic acid. We identified 21 variants by whole exome sequencing, including 4 non-synonymous variants in Korean subjects. The proteins of the wild-type CYP4F11 and the four coding variants (C276R, D315N, D374Y, and D446N) were expressed in Escherichia coli DH5α cells and purified to give cytochrome P450-specific carbon monoxide difference spectra. Wild-type CYP4F2 was also expressed and purified to compare its activity with the CYP4F11 wild-type...
April 15, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28347660/effect-of-genetic-polymorphism-on-the-inhibition-of-dopamine-formation-from-p-tyramine-catalyzed-by-brain-cytochrome-p450-2d6
#19
Toshiro Niwa, Marina Shizuku, Kaori Yamano
The inhibitory effects of steroid hormones, including glucocorticoids such as cortisol, and related compounds on dopamine formation from p-tyramine, catalyzed by cytochrome P450 (CYP) 2D6.2 (Arg296Cys, Ser486Thr) and CYP2D6.10 (Pro34Ser, Ser486Thr) were compared with the effects of those catalyzed by CYP2D6.1 (wild type), to investigate the effect of a CYP2D6 polymorphism on neuroactive amine metabolism in the brain. Inhibition constants (Ki) or 50% inhibitory concentrations of six steroid hormones (cortisol, cortisone, corticosterone, dehydroepiandrosterone, progesterone, and pregnenolone) and quinidine and quinine-typical potent inhibitors of the human CYP2D6 and rat CYP2D subfamily, respectively-toward dopamine formation catalyzed by CYP2D6...
April 15, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28342805/phosphoethanolamine-addition-to-the-heptose-i-of-the-lipopolysaccharide-modifies-the-inner-core-structure-and-has-an-impact-on-the-binding-of-polymyxin-b-to-the-escherichia-coli-outer-membrane
#20
Javier Salazar, Mackarenna Alarcón, Jaime Huerta, Belén Navarro, Daniel Aguayo
Phosphoethanolamine (pEtN) decoration of E. coli Lipopolysaccharide (LPS) provides resistance to the antimicrobial Polymyxin B (PolB). While EptA and EptB enzymes catalyze the addition of pEtN to the Lipid A and Kdo (pEtN-Kdo-Lipid A), EptC catalyzes the pEtN addition to the Heptose I (pEtN-HeptI). In this study, we investigated the contribution of pEtN-HeptI to PolB resistance using eptA/eptB and eptC deficient E. coli K12 and its wild-type parent strains. These mutations were shown to decrease the antimicrobial activity of PolB on cells grown under pEtN-addition inducing conditions...
April 15, 2017: Archives of Biochemistry and Biophysics
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