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Chao Wang, Chongyang Zhao, Lianrui Hu, Hui Chen
Cyanobacterial aldehyde-deformylating oxygenase (cADO) is a nonheme diiron enzyme that catalyzes the conversion of aldehyde to alk(a/e)ne, an important transformation in biofuel research. In this work, we report a highly desired computational study for probing the mechanism of cADO. By combining our QM/MM results with the available (57)Fe Mössbauer spectroscopic data, the gained detailed struc-tural information suggests construction of asymmetry from the symmetric diiron cofactor in aldehyde substrate and O2 activation...
October 24, 2016: Journal of Physical Chemistry Letters
Vishvanath Tiwari
Enzymes catalyze various biochemical functions with high efficiency and specificity. In vitro design of the enzyme leads to novel bioactivity in this natural biomolecule that give answers of some vital questions like crucial residues in binding with substrate, molecular evolution, cofactor specificity etc. Enzyme engineering technology involves directed evolution, rational designing, semi-rational designing, and structure-based designing using chemical modifications. Similarly, combined computational and in vitro evolution approaches together help in artificial designing of novel bioactivity in the natural enzyme...
2016: Frontiers in Chemistry
Alberto Vázquez-Salazar, George Tan, Amanda Stockton, Renato Fani, Arturo Becerra, Antonio Lazcano
The five-membered heterocyclic imidazole group, which is an essential component of purines, histidine and many cofactors, has been abiotically synthesized in different model experiments that attempt to simulate the prebiotic environment. The evolutionary significance of imidazoles is highlighted not only by its presence in nucleic acid components and in histidine, but also by experimental reports of its ability to restore the catalytic activity of ribozymes. However, as of today there are no reports of histidine in carbonaceous chondrites, and although the abiotic synthesis of His reported by Shen et al...
October 22, 2016: Origins of Life and Evolution of the Biosphere
C A Müller, A M Weingartner, A Dennig, A J Ruff, H Gröger, Ulrich Schwaneberg
A novel whole cell cascade for double oxidation of cyclooctane to cyclooctanone was developed. The one-pot oxidation cascade requires only a minimum of reaction components: resting E. coli cells in aqueous buffered medium (=catalyst), the target substrate and oxygen as environmental friendly oxidant. Conversion of cyclooctane was catalysed with high efficiency (50% yield) and excellent selectivity (>94%) to cyclooctanone. The reported oxidation cascade represents a novel whole cell system for double oxidation of non-activated alkanes including an integrated cofactor regeneration...
October 22, 2016: Journal of Industrial Microbiology & Biotechnology
Cristina Mendes de Oliveira, José Eduardo Levi
Human papillomaviruses (HPVs) are the etiologic agents of cervical cancer, the unique human neoplasia that has one single necessary cause. The diversity of HPVs is well described, with 200 HPV types existing as distinct taxonomic units and each receiving an Arabic number. On a clinical basis, they are usually grouped by their site of occurrence and disease associations. Those types inhabiting the anogenital mucosa are more intensively studied and further divided into cancer-associated HPVs, which are termed 'high risk', while those linked to benign proliferative lesions are assigned as 'low risk'...
October 22, 2016: Acta Cytologica
Marli Dercksen, Marinus Duran, Lodewijk IJlst, Wim Kulik, Jos P N Ruiter, Arno van Cruchten, Mendel Tuchman, Ronald J A Wanders
BACKGROUND: N-acetylglutamate synthase (NAGS) plays a key role in the removal of ammonia via the urea cycle by catalyzing the synthesis of N-acetylglutamate (NAG), the obligatory cofactor in the carbamyl phosphate synthetase 1 reaction. Enzymatic analysis of NAGS in liver homogenates has remained insensitive and inaccurate, which prompted the development of a novel method. METHODS: UPLC-MS/MS was used in conjunction with stable isotope (N-acetylglutamic-2,3,3,4,4-d5 acid) dilution for the quantitative detection of NAG produced by the NAGS enzyme...
October 13, 2016: Molecular Genetics and Metabolism
Dworecka-Kaszak Bożena, Dąbrowska Iwona, Kaszak Ilona
The organisms colonizing a living host create together with their host a holobiome. The holobioms are networks of mutualistic interactions between host`s cells and microorganisms communities. The fungi are among these microorganisms and have been also well known to infect human and animals. These organisms are associated with a wide range of diseases as superficial or systemic mycoses. Fungi as colonizers can also modify host physiology and metabolism, energy acquisition, vitamin-cofactor availability, development and function of immune system, and even host behavior...
October 1, 2016: Annals of Parasitology
Cheng-Ming Chiang
BRD4 is an epigenetic regulator and transcription cofactor whose phosphorylation by CK2 and dephosphorylation by PP2A modulates its function in chromatin targeting, factor recruitment, and cancer progression. While the bromodomains of BET family proteins, including BRD4, BRD2, BRD3 and BRDT, have been the primary targets of small compounds such as JQ1, I-BET and MS417 that show promising anticancer effects against some hematopoietic cancer and solid tumors, drug resistance upon prolonged treatment necessitates a better understanding of alternative pathways underlying not only the resistance but also persistent BET protein dependence for identifying new targets and effective combination therapy strategies...
March 2016: Drug Discovery Today. Technologies
Divya Singh, Ghanshyam Upadhyay, Ananya Sengupta, Mohammed A Biplob, Shaleen Chakyayil, Tiji George, Shireen Saleque
Understanding the production and differentiation of megakaryocytes from progenitors is crucial for realizing the biology and functions of these vital cells. Previous gene ablation studies demonstrated the essential role of the transcriptional repressor Gfi1b (growth factor independence 1b) in the generation of both erythroid and megakaryocytic cells. However, our recent work has demonstrated the down-regulation of this factor during megakaryocytic differentiation. In this study we identify two new gene targets of Gfi1b, the cytoskeletal proteins Kindlin3 and Talin1, and demonstrate the inverse expression and functions of these cytoskeletal targets relative to Gfi1b, during megakaryocytic differentiation...
2016: PloS One
Finja Jockenhöfer, Katharina Herberger, Jörg Schaller, Katja Christina Hohaus, Maren Stoffels-Weindorf, Philipp Al Ghazal, Matthias Augustin, Joachim Dissemond
INTRODUCTION: Pyoderma gangrenosum (PG) is a rare neutrophilic, ulcerative skin disease of largely unknown pathophysiology. MATERIAL AND METHODS: In this study, potentially relevant cofactors and comorbidities in patients with PG from three dermatological wound care centers in Germany were evaluated. RESULTS: Of the 121 patients assessed, women (66.9 %) were more frequently affected than men. Patient age ranged from 18 to 96 years (mean 59...
October 2016: Journal der Deutschen Dermatologischen Gesellschaft, Journal of the German Society of Dermatology: JDDG
Zhen Wang, Eric P Chang, Vern L Schramm
Transition path sampling simulations have proposed that human heart lactate dehydrogenase (LDH) employs protein promoting vibrations (PPVs) on the femtosecond (fs) to picosecond (ps) timescale to promote crossing of the chemical barrier. This chemical barrier involves both hydride and proton transfers to pyruvate to form L-lactate, using reduced nicotinamide adenine dinucleotide (NADH) as the cofactor. Here we report experimental evidence from three types of isotope effect experiments that support coupling of the promoting vibrations to barrier crossing and the coincidence of hydride and proton transfer...
October 21, 2016: Journal of the American Chemical Society
C S Bruells, G Marx
Diaphragm function is crucial for patient outcome in the ICU setting and during the treatment period. The occurrence of an insufficiency of the respiratory pump, which is predominantly formed by the diaphragm, may result in intubation after failure of noninvasive ventilation. Especially patients suffering from chronic obstructive pulmonary disease are in danger of hypercapnic respiratory failure. Changes in biomechanical properties and fiber texture of the diaphragm are further cofactors directly leading to a need for intubation and mechanical ventilation...
October 20, 2016: Medizinische Klinik, Intensivmedizin und Notfallmedizin
Mariya Markova, Olga Pivovarova, Silke Hornemann, Stephanie Sucher, Turid Frahnow, Katrin Wegner, Jürgen Machann, Klaus Jürgen Petzke, Johannes Hierholzer, Ralf Lichtinghagen, Christian Herder, Maren Carstensen-Kirberg, Michael Roden, Natalia Rudovich, Susanne Klaus, Ralph Thomann, Rosemarie Schneeweiss, Sascha Rohn, Andreas F H Pfeiffer
BACKGROUND & AIMS: Non-alcoholic fatty liver disease (NAFLD) is associated with increased risk of hepatic, cardiovascular, and metabolic diseases. High-protein diets, rich in methionine and branched chain amino acids (BCAAs), apparently reduce liver fat but may induce insulin resistance. We investigated the effects of diets high in animal protein vs plant protein, which differ in levels of methionine and BCAA, in subjects with type 2 diabetes and NAFLD. We examined levels of liver fat, lipogenic indices, markers of inflammation, serum levels of fibroblast growth factor 21 (FGF21), and activation of signaling pathways in adipose tissue...
October 17, 2016: Gastroenterology
Alfred Weber, Andrea Engelmaier, Gabriele Mohr, Sonja Haindl, Hans Peter Schwarz, Peter L Turecek
BAX 855 (ADYNOVATE) is a PEGylated recombinant factor VIII (rFVIII) that showed prolonged circulatory half-life compared to unmodified rFVIII in hemophilic patients. Here, the development and validation of a novel assay is described that selectively measures the activity of BAX 855 as cofactor for the serine protease factor IX, which actives factor X. This method type, termed modification-dependent activity assay, is based on PEG-specific capture of BAX 855 by an anti-PEG IgG preparation, followed by a chromogenic FVIII activity assay...
September 29, 2016: Journal of Pharmaceutical and Biomedical Analysis
Cristina Puy, Erik I Tucker, Ivan S Ivanov, David Gailani, Stephanie A Smith, James H Morrissey, András Gruber, Owen J T McCarty
INTRODUCTION: Factor (F) XI supports both normal human hemostasis and pathological thrombosis. Activated FXI (FXIa) promotes thrombin generation by enzymatic activation of FXI, FIX, FX, and FV, and inactivation of alpha tissue factor pathway inhibitor (TFPIα), in vitro. Some of these reactions are now known to be enhanced by short-chain polyphosphates (SCP) derived from activated platelets. These SCPs act as a cofactor for the activation of FXI and FV by thrombin and FXIa, respectively...
2016: PloS One
Jinglin Fu, Yuhe Renee Yang, Soma Dhakal, Zhao Zhao, Minghui Liu, Ting Zhang, Nils G Walter, Hao Yan
In nature, the catalytic efficiency of multienzyme complexes highly depends on their spatial organization. The positions and orientations of the composite enzymes are often precisely controlled to facilitate substrate transport between them. Self-assembled DNA nanostructures hold great promise for organizing biomolecules at the nanoscale. Here, we present detailed protocols for exploiting DNA nanostructures as assembly scaffolds that organize the spatial arrangements of multienzyme cascades with control over their relative distance, compartmentalization and substrate diffusion paths...
November 2016: Nature Protocols
Somasundaram Ramasamy, Mohammad Mahfuzul Haque, Mahinda Gangoda, Dennis J Stuehr
The NO synthases (NOS) catalyze a two-step oxidation of L-Arginine (Arg) to generate NO. In the first step, O2 activation involves one electron being provided to the heme by an enzyme-bound 6R-tetrahydro-L-biopterin cofactor (H4 B), which then forms a H4 B radical that must be reduced back to H4 B in order for NOS to continue catalysis. Although an NADPH-derived electron is used to reduce the H4 B radical, how this occurs is unknown. We hypothesized that the NOS flavoprotein domain might reduce the H4 B radical by utilizing the NOS heme porphyrin as a conduit to deliver the electron...
October 19, 2016: FEBS Journal
Evan W Reynolds, Matthew W McHenry, Fabien Cannac, Joshua G Gober, Christopher D Snow, Eric M Brustad
No abstract text is available yet for this article.
October 19, 2016: Journal of the American Chemical Society
Won-Hee Ryu, Forrest S Gittleson, Julianne M Thomsen, Jinyang Li, Mark J Schwab, Gary W Brudvig, André D Taylor
One of the greatest challenges with lithium-oxygen batteries involves identifying catalysts that facilitate the growth and evolution of cathode species on an oxygen electrode. Heterogeneous solid catalysts cannot adequately address the problematic overpotentials when the surfaces become passivated. However, there exists a class of biomolecules which have been designed by nature to guide complex solution-based oxygen chemistries. Here, we show that the heme molecule, a common porphyrin cofactor in blood, can function as a soluble redox catalyst and oxygen shuttle for efficient oxygen evolution in non-aqueous Li-O2 batteries...
October 19, 2016: Nature Communications
Yusuke Matsui, Keisuke Shindo, Kayoko Nagata, Noriyoshi Yoshinaga, Kotaro Shirakawa, Masayuki Kobayashi, Akifumi Takaori-Kondo
HIV type 1 overcomes the host restriction factor apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) proteins by organizing an E3 ubiquitin ligase complex together with viral infectivity factor (Vif) and a host transcription cofactor core binding factor β (CBFβ ). CBFβ is essential for Vif to counteract APOBEC3 by enabling the recruitment of cullin 5 to the complex and increasing steady-state level of Vif protein, however, the mechanisms by which CBFβ up-regulates Vif protein remains unclear...
October 7, 2016: Journal of Biological Chemistry
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