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1. Acetyl-CoA carboxylase in Escherichia coli exhibits a pronounced hysteresis when inhibited by palmitoyl-acyl carrier protein

Author:
Evans, Alexandra; Ribble, Wendy; Schexnaydre, Erin; Waldrop, Grover L.
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
Escherichia coli; Gram-positive bacteria; acetyl coenzyme A; acetyl-CoA carboxylase; biotin; carboxylation; catalytic activity; chemical bonding; fatty acids; hysteresis; malonyl coenzyme A; moieties; multiprotein complexes; pantothenic acid; transport proteins
Abstract:
... Acetyl-CoA carboxylase (ACC) in bacteria is composed of three components: biotin carboxylase, biotin carboxyl carrier protein, and carboxyltransferase. ACC catalyzes the first committed step in fatty acid synthesis: the carboxylation of acetyl-CoA to form malonyl-CoA via a two-step reaction. In the first half-reaction, biotin carboxylase catalyzes the ATP-dependent carboxylation of the vitamin bio ...
DOI:
10.1016/j.abb.2017.10.016

2. ADP-dependent phosphofructokinases from the archaeal order Methanosarcinales display redundant glucokinase activity

Author:
Zamora, Ricardo A.; Gonzalez-Órdenes, Felipe; Castro-Fernández, Victor; Guixé, Victoria
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
Methanococcales; Methanosarcinales; active sites; energy; genes; glucokinase; glycogen; glycolysis; phosphofructokinases; substrate specificity
Abstract:
... The genome of Methanosarcinales organisms presents both ADP-dependent glucokinase and phosphofructokinase genes. However, Methanococcoides burtonii has a truncate glucokinase gene with a large deletion at the C-terminal, where the catalytic GXGD motif is located. Characterization of its phosphofructokinase annotated protein shows that is a bifunctional enzyme able to supply the absence of the gluc ...
DOI:
10.1016/j.abb.2017.09.008

3. Advances in stable isotope assisted labeling strategies with information science

Author:
Kigawa, Takanori
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
amino acids; information science; nuclear magnetic resonance spectroscopy; proteins; solubility; stable isotopes
Abstract:
... Stable-isotope (SI) labeling of proteins is an essential technique to investigate their structures, interactions or dynamics by nuclear magnetic resonance (NMR) spectroscopy. The assignment of the main-chain signals, which is the fundamental first step in these analyses, is usually achieved by a sequential assignment method based on triple resonance experiments. Independently of the triple resonan ...
DOI:
10.1016/j.abb.2017.06.014

4. Amine oxidation by d-arginine dehydrogenase in Pseudomonas aeruginosa

Author:
Ouedraogo, Daniel; Ball, Jacob; Iyer, Archana; Reis, Renata A.G.; Vodovoz, Maria; Gadda, Giovanni
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
Pseudomonas aeruginosa; active sites; arginine; crystallography; hydrides; hydrophobicity; isotopes; oxidation; oxygen; solvents; substrate specificity
Abstract:
... d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is a flavin-dependent oxidoreductase, which is part of a novel two-enzyme racemization system that functions to convert d-arginine to l-arginine. PaDADH contains a noncovalently linked FAD that shows the highest activity with d-arginine. The enzyme exhibits broad substrate specificity towards d-amino acids, particularly with cationic an ...
DOI:
10.1016/j.abb.2017.06.013

5. A new PPARγ/DNA origami biochromatography and offline high performance liquid chromatography-mass spectrometry method for screening PPARγ receptor antagonists from ginsenosides

Author:
Zhou, Jie; Sun, Chong; Meng, Lingchang; Ye, Weiran; Luo, Pei; Sun, Fang; Chen, Shanshan; Xu, Xia
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
DNA; active ingredients; antagonists; drugs; ginsenosides; high performance liquid chromatography; ligands; mass spectrometry; medicinal plants; models; screening
Abstract:
... To rapidly identify novel PPARγ ligands, a robust binding assay amenable to high-efficiency screening toward PPARγ would be desirable. In this study, a new PPARγ assembled on DNA origami (PPARγ/DNA origami) biochromatography drug screening model was constructed and evaluated. The method was used to screen active ingredients acted on PPARγ from the total ginsenosides. The total ginsenosides were ha ...
DOI:
10.1016/j.abb.2017.07.010

6. 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

Author:
Hui, Xian; Hua, Shui-Hong; Wu, Qian-Qian; Li, Heng; Gao, Wen-Yun
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
NADP (coenzyme); biochemical pathways; biosynthesis; epigallocatechin gallate; flavanols; inhibitory concentration 50; medicinal properties; terpenoids
Abstract:
... 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 ...
DOI:
10.1016/j.abb.2017.04.007

7. Application of NMR to studies of intrinsically disordered proteins

Author:
Gibbs, Eric B.; Cook, Erik C.; Showalter, Scott A.
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
genes; hydrogels; nuclear magnetic resonance spectroscopy; post-translational modification; proteins
Abstract:
... 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 s ...
DOI:
10.1016/j.abb.2017.05.008

8. Applications of NMR and computational methodologies to study protein dynamics

Author:
Narayanan, Chitra; Bafna, Khushboo; Roux, Louise D.; Agarwal, Pratul K.; Doucet, Nicolas
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
catalytic activity; computer software; engineering; enzymes; isotope labeling; longevity; nuclear magnetic resonance spectroscopy; proteins
Abstract:
... 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 ...
DOI:
10.1016/j.abb.2017.05.002
PubMed:
28483383
PubMed Central:
PMC5545153

9. Applications of NMR to membrane proteins

Author:
Opella, Stanley J.; Marassi, Francesca M.
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
X-radiation; instrumentation; lipid bilayers; membrane proteins; nuclear magnetic resonance spectroscopy
Abstract:
... 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 l ...
DOI:
10.1016/j.abb.2017.05.011
PubMed:
28529197
PubMed Central:
PMC5657258

10. Applications of NMR to structure determination of RNAs large and small

Author:
Barnwal, Ravi P.; Yang, Fan; Varani, Gabriele
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
molecular weight; nuclear magnetic resonance spectroscopy; nucleotides; ribozymes; transfer RNA
Abstract:
... Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to investigate the structure and dynamics of RNA, because many biologically important RNAs have conformationally flexible structures, which makes them difficult to crystallize. Functional, independently folded RNA domains, range in size between simple stem-loops of as few as 10–20 nucleotides, to 50–70 nucleotides, the size of tRNA a ...
DOI:
10.1016/j.abb.2017.06.003
PubMed:
28600200
PubMed Central:
PMC5555312

11. ATP alters protein folding and function of Escherichia coli uridine phosphorylase

Author:
Liu, Yi-Kai; Lin, Tzu-Hsuan; Liu, Pei-Fen
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
Escherichia coli; adenosine triphosphate; cellular microenvironment; enzyme activity; metabolism; neoplasms; phosphorylase; protein folding; proteins; uracil
Abstract:
... Uridine phosphorylase is one of the critical enzymes in the pyrimidine salvage pathway. Cells regenerate uridine for nucleotide metabolism by incorporating uracil with ribose-1-phosphate with this enzyme. Recent studies indicate that Escherichia coli uridine phosphorylase is destabilized in the presence of ATP. However, the mechanism underlying the destabilization process and its influence on urid ...
DOI:
10.1016/j.abb.2017.09.007

12. Automatic regulation of NF-κB by pHSP70/IκBαm to prevent acute lung injury in mice

Author:
Dong, Hai-Ying; Cui, Yan; Zhang, Bo; Luo, Ying; Wang, Yan-Xia; Dong, Ming-Qing; Liu, Man-Ling; Zhao, Peng-Tao; Niu, Wen; Li, Zhi-Chao
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
cytokines; dose response; gene expression; gene therapy; heart; inflammation; liver; lungs; mice; mutants; plasmids; secretion; signal transduction; transcription factor NF-kappa B; transgenes
Abstract:
... Controlling target gene expression is a vital step in the procedure of gene therapy upon acute lung injury (ALI). Excessive activation of nuclear factor-kappa B (NF-κB) has been the key point of the inflammation overwhelming process in onset of ALI. We designed and tested a variety of plasmid named pHSP70/IκBαm which conditionally carries a mutant inhibitor of kappa B (IκB) transgene to regulate t ...
DOI:
10.1016/j.abb.2017.07.020

13. Biomolecular NMR: Past and future

Author:
Markley, John L.; Westler, William Milo
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
databases; growth and development; nuclear magnetic resonance spectroscopy
Abstract:
... 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 nar ...
DOI:
10.1016/j.abb.2017.05.003
PubMed:
28495511
PubMed Central:
PMC5701516

14. CagL from Helicobacter pylori has ADP-ribosylation activity and exerts partial protective efficacy in mice

Author:
Talluri, Eleonora; Pancotto, Laura; Ruggiero, Paolo; Scarselli, Maria; Balducci, Enrico
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
Helicobacter pylori; bacteria; bioinformatics; enzymes; exotoxins; genes; mice; pathogenesis; prokaryotic cells; vaccination; vaccines
Abstract:
... Mono ADP-ribosyltransferases are a class of functionally conserved enzymes present in prokaryotic and eukaryotic organisms. In prokaryotes, mono ADP-ribose transfer enzymes often represent a family of exotoxins that display activity in a variety of bacteria responsible for causing disease in plants and animals. A bioinformatic approach has allowed us to identify that CagL gene from some Helicobact ...
DOI:
10.1016/j.abb.2017.10.019

15. Cardiotonic actions of quercetin and its metabolite tamarixetin through a digitalis-like enhancement of Ca2+ transients

Author:
Hayamizu, Kengo; Morimoto, Sachio; Nonaka, Miki; Hoka, Sumio; Sasaguri, Toshiyuki
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
anti-inflammatory activity; cAMP-dependent protein kinase; calcium; cardiac output; digoxin; intravenous injection; isoproterenols; metabolites; mice; quercetin; sarcomeres
Abstract:
... The plant-derived flavonoid, quercetin (QCT), has many biological actions, including cardioprotective actions, resulting from its antioxidant and anti-inflammatory effects. In this study, effects of QCT and its metabolites on the contraction and Ca2+ transients (CaT) of mouse single cardiomyocytes were simultaneously measured and compared with those of isoproterenol and digoxin. Furthermore, cardi ...
DOI:
10.1016/j.abb.2017.11.009

16. CFTR modulates RPS27 gene expression using chloride anion as signaling effector

Author:
Valdivieso, Ángel G.; Mori, Consuelo; Clauzure, Mariángeles; Massip-Copiz, Macarena; Santa-Coloma, Tomás A.
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
antagonists; autocrine signaling; chlorides; cystic fibrosis; dose response; fluorescent dyes; gene expression; gene expression regulation; genes; interleukin-1beta; mitogen-activated protein kinase
Abstract:
... In Cystic Fibrosis (CF), the impairment of the CFTR channel activity leads to a variety of alterations, including differential gene expression. However, the CFTR signaling mechanisms remain unclear. Recently, culturing IB3-1 CF cells under different intracellular Cl− concentrations ([Cl−]i), we observed several Cl−-dependent genes and further characterized one of them as RPS27. Thus, we hypothesiz ...
DOI:
10.1016/j.abb.2017.09.014

17. Characterization of Acyl-CoA synthetase isoforms in pancreatic beta cells: Gene silencing shows participation of ACSL3 and ACSL4 in insulin secretion

Author:
Ansari, Israr-ul H.; Longacre, Melissa J.; Stoker, Scott W.; Kendrick, Mindy A.; O'Neill, Lucas M.; Zitur, Laura J.; Fernandez, Luis A.; Ntambi, James M.; MacDonald, Michael J.
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
Lentivirus; acyl coenzyme A; arachidonic acid; enzyme activity; gene silencing; humans; insulin; insulin secretion; islets of Langerhans; long-chain-fatty-acid-CoA ligase; mitochondria; palmitates; phosphatidylethanolamines; phosphatidylserines; proteins; rats; secretory granules
Abstract:
... 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-1832/13 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 i ...
DOI:
10.1016/j.abb.2017.02.001
PubMed:
28193492
PubMed Central:
PMC5445904

18. Characterization of the nuclear import pathway for BLM protein

Author:
Duan, Zhiqiang; Zhao, Jiafu; Xu, Houqiang; Xu, Haixu; Ji, Xinqin; Chen, Xiang; Xiong, Jianming
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
DNA; DNA helicases; guanosine triphosphate; hydrolysis; importins; mutants; nuclear localization signals; physiological transport; small interfering RNA
Abstract:
... Numerous studies have shown that nuclear localization of BLM protein, a member of the RecQ helicases, mediated by nuclear localization signal (NLS) is critical for DNA recombination, replication and transcription, but the mechanism by which BLM protein is imported into the nucleus remains unknown. In this study, the nuclear import pathway for BLM was investigated. We found that nuclear import of B ...
DOI:
10.1016/j.abb.2017.09.019

19. Circadian rhythmicity: A functional connection between differentiated embryonic chondrocyte-1 (DEC1) and small heterodimer partner (SHP)

Author:
Marczak, Marek M.; Yan, Bingfang
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
chromatin; circadian rhythm; energy balance; fatty liver; gel electrophoresis; genes; homeostasis; liver; metabolic diseases; precipitin tests; receptors; risk; site-directed mutagenesis; transcriptional activation; transfection
Abstract:
... Circadian rhythm misalignment has been increasingly recognized to pose health risk for a wide range of diseases, particularly metabolic disorders. The liver maintains metabolic homeostasis and expresses many circadian genes, such as differentiated embryo chondrocyte-1 (DEC1) and small heterodimer partner (SHP). DEC1 is established to repress transcription through E-box elements, and SHP belongs to ...
DOI:
10.1016/j.abb.2017.08.004
PubMed:
28797635
PubMed Central:
PMC5599142

20. Combining NMR and small angle X-ray scattering for the study of biomolecular structure and dynamics

Author:
Mertens, Haydyn D.T.; Svergun, Dmitri I.
Source:
Archives of biochemistry and biophysics 2017
ISSN:
0003-9861
Subject:
X-radiation; ligands; nuclear magnetic resonance spectroscopy; particle size
Abstract:
... 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 elucid ...
DOI:
10.1016/j.abb.2017.05.005
PubMed:
28501583
PubMed Central:
PMC5553349