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Archives of Biochemistry and Biophysics

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https://www.readbyqxmd.com/read/28315301/metabolites-of-2-3-diketogulonate-delay-peroxidase-action-and-induce-non-enzymic-h2o2-generation-potential-roles-in-the-plant-cell-wall
#1
Anna Kärkönen, Rebecca A Dewhirst, C Logan Mackay, Stephen C Fry
A proportion of the plant's l-ascorbate (vitamin C) occurs in the apoplast, where it and its metabolites may act as pro-oxidants and anti-oxidants. One ascorbate metabolite is 2,3-diketogulonate (DKG), preparations of which can non-enzymically generate H2O2 and delay peroxidase action on aromatic substrates. As DKG itself generates several by-products, we characterised these and their ability to generate H2O2 and delay peroxidase action. DKG preparations rapidly produced a by-product, compound (1), with λmax 271 and 251 nm at neutral and acidic pH respectively...
March 14, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28315300/interaction-of-glyceraldehyde-3-phosphate-dehydrogenase-and-heme-the-relevance-of-its-biological-function
#2
Yi Huang, Pengfei Zhang, Zhen Yang, Peipei Wang, Hailing Li, Zhonghong Gao
GAPDH was speculated to function as a transient trap to reduce the potential toxicity of free heme by a specific and reversible binding with heme. Up to now, there has been lack of studies focused on this effect. In this paper, the efficiency of GAPDH-heme complex on catalyzing protein carbonylation and nitration, the cross-linking of heme to protein formation, and cytotoxicity of GAPDH-heme were studied. It was found that the binding of GAPDH could inhibit H2O2-mediated degradation of heme. Peroxidase activity of GAPDH-heme complex was higher than that of free heme, but significantly lower than that of HSA-heme...
March 14, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28300536/hydroxylation-of-4-hydroxyphenylethylamine-derivatives-by-r263-variants-of-the-oxygenase-component-of-p-hydroxyphenylacetate-3-hydroxylase
#3
Pirom Chenprakhon, Taweesak Dhammaraj, Rattikan Chantiwas, Pimchai Chaiyen
p-hydroxyphenylacetate 3-hydroxylase from Acinetobacter baumannii catalyzes the hydroxylation of p-hydroxyphenylacetate (HPA) to yield 3,4-dihydroxyphenylacetate (DHPA). In this study, we investigated whether variants of the oxygenase component (C2) could catalyze hydroxylation of 4-hydroxyphenylethylamines to synthesize catecholamine derivatives. Single turnover product analysis showed that the R263D variant can catalyze hydroxylation of tyramine to form dopamine with the highest yield (57%). The enzyme was also found to have dual substrate charge specificity because it can also maintain reasonable hydroxylation efficiency of HPA (86%)...
March 12, 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
#4
Octavio Monasterio, Esteban Nova, Rodrigo Diaz-Espinoza
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...
March 10, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28283321/minimized-natural-versions-of-fungal-ribotoxins-show-improved-active-site-plasticity
#5
Moisés Maestro-López, Miriam Olombrada, Lucía García-Ortega, Daniel Serrano-González, Javier Lacadena, Mercedes Oñaderra, José G Gavilanes, Álvaro Martínez-Del-Pozo
Fungal ribotoxins are highly specific extracellular RNases which cleave a single phosphodiester bond at the ribosomal sarcin-ricin loop, inhibiting protein biosynthesis by interfering with elongation factors. Most ribotoxins show high degree of conservation, with similar sizes and amino acid sequence identities above 85%. Only two exceptions are known: hirsutellin A and anisoplin, produced by the entomopathogenic fungi Hirsutella thompsonii and Metarhizium anisopliae, respectively. Both proteins are similar but smaller than the other known ribotoxins (130 vs 150 amino acids), displaying only about 25% sequence identity with them...
March 7, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28274616/interaction-mechanism-of-insulin-like-peptide-5-with-relaxin-family-peptide-receptor-4
#6
Meng-Jun Hu, Dian Wei, Xiao-Xia Shao, Jia-Hui Wang, Ya-Li Liu, Zeng-Guang Xu, Zhan-Yun Guo
Insulin-like peptide 5 (INSL5) is a gut peptide hormone belonging to the insulin/relaxin superfamily. It is implicated in the regulation of food intake and glucose homeostasis by activating relaxin family peptide receptor 4 (RXFP4). Previous studies have suggested that the B-chain is important for INSL5 activity against RXFP4. However, functionalities of the B-chain residues have not yet been systematically studied. In the present work, we conducted alanine-scanning mutagenesis of the B-chain residues of human INSL5 to obtain an overview of their contributions...
March 6, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28263718/nmr-based-automated-protein-structure-determination
#7
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
#8
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
#9
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/28257787/red-ox-states-of-human-protein-disulfide-isomerase-regulate-binding-affinity-of-17-beta-estradiol
#10
Razieh Karamzadeh, Mohammad Hossein Karimi-Jafari, Ali Akbar Saboury, Ghasem Hosseini Salekdeh, Ali Akbar Moosavi-Movahedi
Human protein disulfide isomerase (hPDI) is a key redox-regulated thiol-containing protein operating as both oxidoreductase and molecular chaperone in the endoplasmic reticulum of cells. hPDI thiol-disulfide interchange reactions lead to the adoption of two distinct red/ox conformations with different substrate preferences. hPDI also displays high binding capacity for some endogenous steroid hormones including 17 beta-estradiol (E2) and thus contributes to the regulation of their intracellular concentration, storage and actions...
February 28, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28249720/targeting-thioredoxin-reductase-by-plumbagin-contributes-to-inducing-apoptosis-of-hl-60%C3%A2-cells
#11
Junmin Zhang, Shoujiao Peng, Xinming Li, Ruijuan Liu, Xiao Han, Jianguo Fang
Plumbagin (PLB), a natural naphthoquinone from the traditional folk medicines Plumbago zeylanica, Dionaea muscipula, or Nepenthes gracilis, has been documented possessing a wide variety of pharmacological activities. Although PLB demonstrates anticancer activity in multiple types of malignant cells, the cellular targets of PLB have not been well defined and remained only partially understood. We reported here that PLB selectively inhibits TrxR and elicits reactive oxygen species in human promyelocytic leukemia HL-60 cells, which leads to elevation of GSSG/GSH ratio and decrease of cellular thiol pool...
February 27, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28238672/thermodynamics-of-interactions-between-mammalian-cytochromes-p450-and-b5
#12
Evgeny Yablokov, Anna Florinskaya, Alexei Medvedev, Gennady Sergeev, Natallia Strushkevich, Alexander Luschik, Tatsiana Shkel, Irina Haidukevich, Andrei Gilep, Sergey Usanov, Alexis Ivanov
Cytochromes P450 (CYPs) play an important role in the metabolism of xenobiotics and various endogenous substrates. Being a crucial component of the microsomal monooxygenase system, CYPs are involved in numerous protein-protein interactions. However, mechanisms underlying molecular interactions between components of the monooxygenase system still need better characterization. In this study thermodynamic parameters of paired interactions between mammalian CYPs and cytochromes b5 (CYB5) have been evaluated using a Surface Plasmon Resonance (SPR) based biosensor Biacore 3000...
February 24, 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
#13
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
#14
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/28235466/trifluoroethanol-induced-conformational-transition-of-the-c-terminal-sterile-alpha-motif-sam-of-human-p73
#15
José L Neira, Ana Cámara-Artigas
The alpha splice variant of p73 (p73α), a homologue of the tumour suppressor p53, has at its C terminus a sterile alpha motif (SAM); this domain, SAMp73, is involved in lipid binding and it is thought to mediate in protein-protein interactions. As SAMp73 is a 68-residue-long helical bundle, it could be a good model to study the (2,2,2-trifluoroethanol) TFE-induced conformational transitions of α-helical proteins. Furthermore, as SAMp73 binds to lipids through a well-known polypeptide patch, we can test whether TFE is a good mimic of lipids and membranes...
February 21, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28193492/characterization-of-acyl-coa-synthetase-isoforms-in-pancreatic-beta-cells-gene-silencing-shows-participation-of-acsl3-and-acsl4-in-insulin-secretion
#16
Israr-Ul H Ansari, Melissa J Longacre, Scott W Stoker, Mindy A Kendrick, Lucas M O'Neill, Laura J Zitur, Luis A Fernandez, James M Ntambi, Michael J MacDonald
Long-chain acyl-CoA synthetases (ACSLs) convert fatty acids to fatty acyl-CoAs to regulate various physiologic processes. We characterized the ACSL isoforms in a cell line of homogeneous rat beta cells (INS-1 832/13 cells) and human pancreatic islets. ACSL4 and ACSL3 proteins were present in the beta cells and human and rat pancreatic islets and concentrated in insulin secretory granules and less in mitochondria and negligible in other intracellular organelles. ACSL1 and ACSL6 proteins were not seen in INS-1 832/13 cells or pancreatic islets...
February 11, 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
#17
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/28137422/the-lncrna-uca1-interacts-with-mir-182-to-modulate-glioma-proliferation-and-migration-by-targeting-iaspp
#18
Zongze He, Yujue Wang, Guangfu Huang, Qi Wang, Dongdong Zhao, Longyi Chen
Long non-coding RNA (lncRNA) urothelial carcinoma associated 1 (UCA1) has been reported to be involved in the development and progression of many types of tumors including breast cancer, gastric cancer, and bladder cancer. However, the exact effects and molecular mechanisms of UCA1 in glioma progression remain unclear up to now. In this study, we firstly found that UCA1 was upregulated in glioma tumor samples and negatively correlated with survival time. Then, we investigated the role of UCA1 in human glioma cell lines...
January 27, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28132757/oligomerization-affects-the-kinetics-and-thermodynamics-of-the-interaction-of-a-bowman-birk-inhibitor-with-proteases
#19
G D Brand, D A T Pires, J R Furtado, A Cooper, S M Freitas, C Bloch
The black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) forms concentration dependent homomultimers, as previously demonstrated by Light scattering and Atomic Force Microscopy. Considering that these self-aggregates might influence their binding to cognate enzymes, we investigated the interaction of BTCI at picomolar concentrations using surface immobilized Chymotrypsin (α-CT) and Trypsin (T) by Surface Plasmon Resonance. Our results indicate that BTCI has subnanomolar affinity to both immobilized enzymes, which is approximately two orders of magnitude higher than previously reported...
January 26, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28131773/redox-sensing-molecular-mechanism-of-an-iron-metabolism-regulatory-protein-fbxl5
#20
Yaozhu Wei, Hong Yuan, Pengbiao Xu, Xiangshi Tan
FBXL5 is a subunit of the SCF(FBXL5) ubiquitin ligase complex that targets the proteasomal degradation of iron regulatory protein IRP2, which is an important regulator in iron metabolism. The degradation of FBXL5 itself is regulated in an iron- and oxygen-responsive manner through its diiron center containing Hr-like domain. Although the crystal structure of the Hr-like domain of FBXL5 and its degradation based on iron/oxygen sensing has been reported, the redox sensing molecular mechanism is still not clear...
January 25, 2017: Archives of Biochemistry and Biophysics
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