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Archives of Biochemistry and Biophysics

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https://www.readbyqxmd.com/read/28529198/nitroalkane-oxidase-structure-and-mechanism
#1
REVIEW
Paul F Fitzpatrick
The flavoprotein nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones, releasing nitrite and transferring electrons to O2 to form H2O2. A combination of solution and structural analyses have provided a detailed understanding of the mechanism of this enzyme.
May 18, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28529197/applications-of-nmr-to-membrane-proteins
#2
Stanley J Opella, Francesca M Marassi
Membrane proteins present a challenge for structural biology. In this article, we review some of the recent developments that advance the application of NMR to membrane proteins, with emphasis on structural studies in detergent-free, lipid bilayer samples that resemble the native environment. NMR spectroscopy is not only ideally suited for structure determination of membrane proteins in hydrated lipid bilayer membranes, but also highly complementary to the other principal techniques based on X-ray and electron diffraction...
May 18, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28528195/repulsive-surfaces-and-lamellar-lubrication-of-synovial-joints
#3
Zenon Pawlak, Kehinde Q Yusuf, Raghuvir Pai, Wieslaw Urbaniak
Surface-active phospholipid (SAPL) secreted in the synovial joint plays an important role in cartilage integrity. In healthy joints, phospholipid multibilayers coat the cartilage surface, providing boundary lamellar-repulsive hydration lubrication. Current mechanism for lubrication of synovial joints, as well as the physical and chemical nature of the cartilage surface is discussed. Friction between phospholipid (PL) bilayers attached to cartilage surfaces is considered including a discussion on the recent observation of an extreme friction reduction as a consequence of a less charged hydrophilic cartilage surface...
May 17, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28526426/the-effects-of-troglitazone-on-ampk-in-hepg2-cells
#4
Katherine M Allen, Kimberly A Coughlan, Fabliha N Mahmood, Rudy J Valentine, Neil B Ruderman, Asish K Saha
AMP-activated protein kinase (AMPK) is an enzyme crucial in cellular metabolism found to be inhibited in many metabolic diseases including type 2 diabetes. Thiazolidinediones (TZDs) are a class of anti-diabetic drug known to activate AMPK through increased phosphorylation at Thr(172), however there has been no research to date on whether they have any effect on inhibition of AMPK's lesser known site of inhibition, Ser(485/491). HepG2 cells were treated with troglitazone and phosphorylation of AMPK was found to increase at both Thr(172) and Ser(485) in a dose- and time-dependent manner...
May 16, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28522117/characterization-of-cu-ii-reconstituted-acc-oxidase-using-experimental-and-theoretical-approaches
#5
Nadia El Bakkali-Tahéri, Sybille Tachon, Maylis Orio, Sylvain Bertaina, Marlène Martinho, Viviane Robert, Marius Réglier, Thierry Tron, Pierre Dorlet, A Jalila Simaan
1-Aminocyclopropane-1-carboxylic acid oxidase (ACCO) is a non heme iron(II) containing enzyme that catalyzes the final step of the ethylene biosynthesis in plants. The iron(II) ion is bound in a facial triad composed of two histidines and one aspartate (H177, D179 and H234). Several active site variants were generated to provide alternate binding motifs and the enzymes were reconstituted with copper(II). Continuous wave (cw) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopies as well as Density Functional Theory (DFT) calculations were performed and models for the copper(II) binding sites were deduced...
May 15, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28502466/purification-and-site-directed-mutagenesis-of-linoleate-9s-dioxygenase-allene-oxide-synthase-of-fusarium-oxysporum-confirms-the-oxygenation-mechanism
#6
Yang Chen, Fredrik Jernerén, Ernst H Oliw
Plants and fungi form jasmonic acid from α-linolenic acid. The first two steps of biosynthesis in plants occur by sequential transformation by 13S-lipoxygenase and allene oxide synthase (AOS). The biosynthesis in fungi may follow this classical scheme, but the only fungal AOS discovered so far are cytochromes P450 (CYP) fused to 8- and 9-dioxygenases (DOX). In the present report, we purified recombinant 9S-DOX-AOS of Fusarium oxysporum from cell lysate by cobalt affinity chromatography to near homogeneity and studied key residues by site-directed mutagenesis...
May 11, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28502465/application-of-nmr-to-studies-of-intrinsically-disordered-proteins
#7
Eric B Gibbs, Erik C Cook, Scott A Showalter
The prevalence of intrinsically disordered protein regions, particularly in eukaryotic proteins, and their clear functional advantages for signaling and gene regulation have created an imperative for high-resolution structural and mechanistic studies. NMR spectroscopy has played a central role in enhancing not only our understanding of the intrinsically disordered native state, but also how that state contributes to biological function. While pathological functions associated with protein aggregation are well established, it has recently become clear that disordered regions also mediate functionally advantageous assembly into high-order structures that promote the formation of membrane-less sub-cellular compartments and even hydrogels...
May 11, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28501584/thiamine-potentiates-chemoprotective-effects-of-ibuprofen-in-den-induced-hepatic-cancer-via-alteration-of-oxidative-stress-and-inflammatory-mechanism
#8
Muhammad Afzal, Imran Kazmi, Ruqaiyah Khan, Poonam Rana, Vikas Kumar, Fahad A Al-Abbasi, Mazin Zamzami, Firoz Anwar
Present study, was an effort to scrutinize the molecular and biochemical role of ibuprofen and thiamine combination in diethylnitrosamine (DEN)-induced HCC in Wistar rats. Single intraperitoneal injection of DEN (200 mg/kg) was used for induction of HCC in rats. The rats were divided into eight various groups. DEN induced rats were treated with pure ibuprofen (40 mg/kg) and thiamine in combination for the period of 12th weeks. The protocol was terminated after the 16th week. Exposure of DEN up-regulated the levels of different serum biochemical parameters, antioxidant enzyme level, Alfa-fetoprotein (AFP) and reduced the level of High density lipoprotein (HDL) in Wistar rats along with the alteration in pro-inflammatory cytokines viz...
May 10, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28501583/combining-nmr-and-small-angle-x-ray-scattering-for-the-study-of-biomolecular-structure-and-dynamics
#9
Haydyn D T Mertens, Dmitri I Svergun
Small-angle X-rays scattering (SAXS) and Nuclear Magnetic Resonance (NMR) are established methods to analyze the structure and structural transitions of biological macromolecules in solution. Both methods are directly applicable to near-native macromolecular solutions and allow one to study structural responses to physical and chemical changes or ligand additions. Whereas SAXS is applied to elucidate overall structure, interactions and flexibility over a wide range of particle sizes, NMR yields atomic resolution detail for moderately sized macromolecules...
May 10, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28499743/resolution-of-the-uncertainty-in-the-kinetic-mechanism-for-the-trans-3-chloroacrylic-acid-dehalogenase-catalyzed-reaction
#10
Jamison P Huddleston, Susan C Wang, Kenneth A Johnson, Christian P Whitman
trans- and cis-3-Chloroacrylic acid dehalogenase (CaaD and cis-CaaD, respectively) catalyze the hydrolytic dehalogenation of their respective isomers and represent key steps in the bacterial conversion of 1,3-dichloropropene to acetaldehyde. In prior work, a kinetic mechanism for the CaaD-catalyzed reaction could not be unequivocally determined because (1) the order of product release could not be determined and (2) the fluorescence factor for the enzyme species, E*PQ (where P = bromide and Q = malonate semialdehyde, the two products of the reaction) could not be assigned...
May 10, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28495512/modulation-of-casc2-mir-21-pten-pathway-sensitizes-cervical-cancer-to-cisplatin
#11
Yeqian Feng, Wen Zou, Chunhong Hu, Guiyuan Li, Shenghua Zhou, Yan He, Fang Ma, Chao Deng, Lili Sun
Cisplatin (DDP) -based chemotherapy is a standard strategy for cervical cancer, while chemoresistance remains a challenge. Recent evidence highlights the crucial regulatory roles of long non-coding RNAs (lncRNA) in tumor biology. However, the roles and regulatory mechanisms of the novel lncRNA, cancer susceptibility candidate 2 (CASC2), in cervical cancer tumorigenesis and chemoresistance are poorly understood. In this study, CASC2 expression was down-regulated in cervical cancer tissues, and was related to a shorter survival time and poorer clinicopathologic features...
May 8, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28495511/biomolecular-nmr-past-and-future
#12
John L Markley, William Milo Westler
The editors of this special volume suggested this topic, presumably because of the perspective lent by our combined >90-year association with biomolecular NMR. What follows is our personal experience with the evolution of the field, which we hope will illustrate the trajectory of change over the years. As for the future, one can confidently predict that it will involve unexpected advances. Our narrative is colored by our experience in using the NMR Facility for Biomedical Studies at Carnegie-Mellon University (Pittsburgh) and in developing similar facilities at Purdue (1977-1984) and the University of Wisconsin-Madison (1984-)...
May 8, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28483383/applications-of-nmr-and-computational-methodologies-to-study-protein-dynamics
#13
REVIEW
Chitra Narayanan, Khushboo Bafna, Louise D Roux, Pratul K Agarwal, Nicolas Doucet
Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization...
May 5, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28456640/adrenic-acid-as-an-inflammation-enhancer-in-non-alcoholic-fatty-liver-disease
#14
Saut Nababan, Shin Nishiumi, Yuki Kawano, Takashi Kobayashi, Masaru Yoshida, Takeshi Azuma
BACKGROUND: This study was designed to identify novel links between lipid species and disease progression in non-alcoholic fatty liver disease (NAFLD). METHODS: We analyzed lipid species in the liver and plasma of db/db mice fed a choline-deficient l-amino acid-defined, high-fat diet (CDAHFD) using liquid chromatography/mass spectrometry (LC/MS). An in vitro experiment was performed using HepG2 cells stimulated with recombinant human TNFα or IL1β. The expression of steatosis-, inflammation-, and fibrosis-related genes were analyzed...
April 26, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28263718/nmr-based-automated-protein-structure-determination
#15
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
#16
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
#17
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/28461187/hyperthermophilic-l-asparaginase-bypasses-monomeric-intermediates-during-folding-to-retain-cooperativity-and-avoid-amyloid-assembly
#18
Dushyant K Garg, Bishwajit Kundu
In obligate dimeric proteins of hyperthermophilic origin the question whether the native dimer is obtained by association of folded monomers or through concomitant folding and assembly of subunits has intrigued researchers. To find an answer we studied the folding of a dimeric enzyme l-asparaginase from Pyrococcus furiosus (PfA) for which we reported earlier that it unfolds cooperatively without populating folded monomeric intermediates. However, in the present study we report the finding of a folded monomeric intermediate of PfA under acidic condition...
May 15, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28442401/trib3-downregulation-enhances-doxorubicin-induced-cytotoxicity-in-gastric-cancer-cells
#19
I-Jung Wu, Rong-Jaan Lin, Hsin-Chiao Wang, Tein-Ming Yuan, Show-Mei Chuang
TRIB3, which is a pseudokinase known to regulate multiple pro-survival pathways, appears to be a potential therapeutic target for the treatment of human tumors. However, its precise role in cancer is controversial, as TRIB3 protein levels have been associated with both good and poor prognosis in cancer patients. Here, we investigated the significance of TRIB3 expression in the survival of gastric cancer cells exposed to anticancer drugs. We found that the tested anticancer drug, doxorubicin, induced cytotoxicity by decreasing TRIB3 transcription, which was followed by apoptotic cell death...
May 15, 2017: Archives of Biochemistry and Biophysics
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
#20
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...
May 15, 2017: Archives of Biochemistry and Biophysics
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