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Biochimica et Biophysica Acta

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https://www.readbyqxmd.com/read/29343430/cardiolipin-synthesizing-enzymes-form-a-complex-that-interacts-with-cardiolipin-dependent-membrane-organizing-proteins
#1
Mauro Serricchio, Adriano Vissa, Peter K Kim, Christopher M Yip, G A McQuibban
The mitochondrial glycerophospholipid cardiolipin plays important roles in mitochondrial biology. Most notably, cardiolipin directly binds to mitochondrial proteins and helps assemble and stabilize mitochondrial multi-protein complexes. Despite their importance for mitochondrial health, how the proteins involved in cardiolipin biosynthesis are organized and embedded in mitochondrial membranes has not been investigated in detail. Here we show that human PGS1 and CLS1 are constituents of large protein complexes...
January 14, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29343429/translational-control-of-human-acetyl-coa-carboxylase-1-mrna-is-mediated-by-an-internal-ribosome-entry-site-in-response-to-er-stress-serum-deprivation-or-hypoxia-mimetic-cocl2
#2
Fabrizio Damiano, Mariangela Testini, Romina Tocci, Gabriele V Gnoni, Luisa Siculella
Acetyl-CoA carboxylase 1 (ACC1) is a cytosolic enzyme catalyzing the rate limiting step in de novo fatty acid biosynthesis. There is mounting evidence showing that ACC1 is susceptible to dysregulation and that it is over-expressed in liver diseases associated with lipid accumulation and in several cancers. In the present study, ACC1 regulation at the translational level is reported. Using several experimental approaches, the presence of an internal ribosome entry site (IRES) has been established in the 5' untranslated region (5' UTR) of the ACC1 mRNA...
January 14, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29341928/a-novel-brown-adipocyte-enriched-long-non-coding-rna-that-is-required-for-brown-adipocyte-differentiation-and-sufficient-to-drive-thermogenic-gene-program-in-white-adipocytes
#3
Yan Xiong, Feng Yue, Zhihao Jia, Yun Gao, Wen Jin, Keping Hu, Yong Zhang, Dahai Zhu, Gongshe Yang, Shihuan Kuang
The thermogenic activities of brown and beige adipocytes can be exploited to reduce energy surplus and counteract obesity. Recent RNA sequencing studies have uncovered a number of long noncoding RNAs (lncRNAs) uniquely expressed in white and brown adipose tissues (WAT and BAT), but whether and how these lncRNAs function in adipogenesis remain largely unknown. Here, we report the identification of a novel brown adipocyte-enriched LncRNA (AK079912), and its nuclear localization, function and regulation. The expression of AK079912 increases during brown preadipocyte differentiation and in response to cold-stimulated browning of white adipocytes...
January 13, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29339327/the-chaperonin-cct-promotes-the-formation-of-fibrillar-aggregates-of-%C3%AE-tubulin
#4
Luis Pouchucq, Pablo Lobos-Ruiz, Gisela Araya, José María Valpuesta, Octavio Monasterio
The type II chaperonin CCT is involved in the prevention of the pathogenesis of numerous human misfolding disorders, as it sequesters misfolded proteins, blocks their aggregation and helps them to achieve their native state. In addition, it has been reported that CCT can prevent the toxicity of non-client amyloidogenic proteins by the induction of non-toxic aggregates, leading to new insight in chaperonin function as an aggregate remodeling factor. Here we add experimental evidence to this alternative mechanism by which CCT actively promotes the formation of conformationally different aggregates of γ-tubulin, a non-amyloidogenic CCT client protein, which are mediated by specific CCT-γ-tubulin interactions...
January 12, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29339121/hsf1-in-association-with-morc2-downregulates-argbp2-via-the-prc2-family-in-gastric-cancer-cells
#5
Yuxin Tong, Yan Li, Hui Gu, Chunyu Wang, Funan Liu, Yangguang Shao, Feng Li
Arg Kinase-binding protein 2 (ArgBP2) is considered to be a scaffold protein that coordinates multiple signaling pathways converging on cell adhesion and actin cytoskeletal organization. It also plays an important role in blocking cancer metastasis as a potential tumor suppressor. However, its regulation mechanisms in tumor migration, especially in gastric cancer, are not fully understood. Here, we identified an ArgBP2 enhancer and showed that heat shock factor 1 (HSF1) directly interacted with microrchidia CW-type zinc finger 2 (MORC2) and bound to the enhancer of ArgBP2...
January 12, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29339082/water-mediated-interactions-enable-smooth-substrate-transport-in-a-bacterial-efflux-pump
#6
Attilio Vittorio Vargiu, Venkata Krishnan Ramaswamy, Ivana Malvacio, Giuliano Malloci, Ulrich Kleinekathöfer, Paolo Ruggerone
BACKGROUND: Efflux pumps of the Resistance-Nodulation-cell Division superfamily confer multi-drug resistance to Gram-negative bacteria. The most-studied polyspecific transporter belonging to this class is the inner-membrane trimeric antiporter AcrB of Escherichia coli. In previous studies, a functional rotation mechanism was proposed for its functioning, according to which the three monomers undergo concerted conformational changes facilitating the extrusion of substrates. However, the molecular determinants and the energetics of this mechanism still remain unknown, so its feasibility must be proven mechanistically...
January 12, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29339081/disorder-to-order-transitions-in-the-molten-globule-like-golgi-reassembly-and-stacking-protein
#7
Luís F S Mendes, Luis G M Basso, Patricia S Kumagai, Raquel Fonseca-Maldonado, Antonio J Costa-Filho
BACKGROUND: Golgi Reassembly and Stacking Proteins (GRASPs) are widely spread among eukaryotic cells (except plants) and are considered as key components in both the stacking of the Golgi cisternae and its lateral connection. Furthermore, GRASPs were also proved essential in the unconventional secretion pathway of several proteins, even though the mechanism remains obscure. It was previously observed that the GRASP homolog in Cryptococcus neoformans has a molten globule-like behavior in solution...
January 12, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29338975/critical-effects-of-polar-fluorescent-probes-on-the-interaction-of-dha-with-popc-supported-lipid-bilayers
#8
Kiera R Flynn, Alessandra Sutti, Lisandra L Martin, M Leigh Ackland, Angel A J Torriero
The understanding of lipid bilayer structure and function has been advanced by the application of molecular fluorophores. However, the effects of these probe molecules on the physicochemical properties of membranes being studied are poorly understood. A quartz crystal microbalance with dissipation monitoring instrument was used in this work to investigate the impact of two commonly used fluorescent probes, 1-palmitoyl-2-{12-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]dodecanoyl}-sn-glycero-3-phosphocholine (NBD-PC) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(lissamine rhodamine-B-sulfonyl) (Lis-Rhod PE), on the formation and physicochemical properties of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine supported lipid bilayer (POPC-SLB)...
January 12, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29337275/the-o-%C3%AE-linked-n-acetylglucosaminylation-of-the-lamin-b-receptor-and-its-impact-on-dna-binding-and-phosphorylation
#9
Caroline Smet-Nocca, Adeline Page, François-Xavier Cantrelle, Eleni Nikolakaki, Isabelle Landrieu, Thomas Giannakouros
Lamin B Receptor (LBR) is an integral protein of the interphase inner nuclear membrane that is implicated in chromatin anchorage to the nuclear envelope. Phosphorylation of a stretch of arginine-serine (RS) dipeptides in the amino-terminal nucleoplasmic domain of LBR regulates the interactions of the receptor with other nuclear proteins, DNA and RNA and thus modulates tethering of heterochromatin to the nuclear envelope. While phosphorylation has been extensively studied, very little is known about other post-translational modifications of the protein...
January 11, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29337209/the-role-of-d-allo-isoleucine-in-the-deposition-of-the-anti-leishmania-peptide-bombinin-h4-as-revealed-by-31p-solid-state-nmr-vcd-spectroscopy-and-md-simulation
#10
Batsaikhan Mijiddorj, Shiho Kaneda, Hisako Sato, Yuki Kitahashi, Namsrai Javkhlantugs, Akira Naito, Kazuyoshi Ueda, Izuru Kawamura
Bombinin H4 is an antimicrobial peptide that was isolated from the toad Bombina variegata. Bombinin H family peptides are active against gram-positive, gram-negative bacteria, and fungi as well as the parasite Leishmania. Among them, bombinin H4 (H4), which contains d-allo-isoleucine (d-allo-Ile) as the second residue in its sequence, is the most active, and its l-isomer is bombinin H2 (H2). H4 has a significantly lower LC50 than H2 against Leishmania. However, the atomic-level mechanism of the membrane interaction and higher activity of H4 has not been clarified...
January 11, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29337190/binding-of-ferredoxin-to-algal-photosystem-i-involves-a-single-binding-site-and-is-composed-of-two-thermodynamically-distinct-events
#11
Pini Marco, Marina Kozuleva, Haviva Eilenberg, Yuval Mazor, Peter Gimeson, Andrey Kanygin, Kevin Redding, Iftach Yacoby
Despite the impressive progress made in recent years in understanding the early steps in charge separation within the photosynthetic reaction centers, our knowledge of how ferredoxin (Fd) interacts with the acceptor side of photosystem I (PSI) is not as well developed. Fd accepts electrons after transiently docking to a binding site on the acceptor side of PSI. However, the exact location, as well as the stoichiometry, of this binding have been a matter of debate for more than two decades. Here, using Isothermal Titration Calorimetry (ITC) and purified components from wild type and mutant strains of the green algae Chlamydomonas reinhardtii we show that PSI has a single binding site for Fd, and that the association consists of two distinct binding events, each with a specific association constant...
January 11, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29337112/molecular-heterogeneity-in-diffuse-large-b-cell-lymphoma-and-its-implications-in-clinical-diagnosis-and-treatment
#12
REVIEW
Lingchuan Guo, Pei Lin, Hui Xiong, Shichun Tu, Gang Chen
Over half of patients with diffuse large B-cell lymphoma (DLBCL) can be cured by standard R-CHOP treatment (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone). However, the remaining patients are refractory and ultimately succumb to progressive or relapsed disease. During the past decade, there has been significant progress in the understanding of molecular mechanisms in DLBCL, largely owing to collaborative efforts in large-scale gene expression profiling and deep sequencing, which have identified genetic alterations critical in lymphomagenesis through activation of key signaling transduction pathways in DLBCL...
January 11, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29331638/comparative-analysis-of-membrane-protein-structure-databases
#13
REVIEW
Kentaro Shimizu, Wei Cao, Gull Saad, Michiru Shoji, Tohru Terada
BACKGROUND: Membrane proteins play important roles in cell survival and cell communication, as they function as transporters, receptors, anchors and enzymes. They are also potential targets for drugs that block receptors or inhibit enzymes related to diseases. Although the number of known structures of membrane proteins is still small relative to the size of the proteome as a whole, many new membrane protein structures have been determined recently. SCOPE OF THE ARTICLE: We compared and analyzed the widely used membrane protein databases, mpstruc, Orientations of Proteins in Membranes(OPM), and PDBTM, as well as the extended dataset of mpstruc based on sequence similarity, the PDB structures whose classification field indicates that they are "membrane proteins" and the proteins with Structural Classification of Proteins (SCOP) class-f domains...
January 10, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29331509/selenolanthionine-is-the-major-water-soluble-selenium-compound-in-the-selenium-tolerant-plant-cardamine-violifolia
#14
Eszter Borbála Both, Shuxun Shao, Jiqian Xiang, Zsuzsa Jókai, Hongqing Yin, Yafeng Liu, Anna Magyar, Mihály Dernovics
BACKGROUND: Selenium hyperaccumulation in plants often involves the synthesis of non-proteinaceous methylated selenoamino acids serving for the elimination of excess selenium from plant metabolism to protect plant homeostasis. METHODS: Our study aimed at the identification of the main selenium species of the selenium hyperaccumulator plant Cardamine violifolia (Brassicaceae) that grows in the wild in the seleniferous region of Enshi, China. A sample of this plant (3...
January 10, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29331333/influences-of-conformations-of-peptides-on-stereoinversions-and-or-isomerizations-of-aspartic-acid-residues
#15
Akifumi Oda, Tomoki Nakayoshi, Shuichi Fukuyoshi, Eiji Kurimoto, Ohgi Takahashi
Recently, non-enzymatic stereoinversions of aspartic acid (Asp) residues in proteins and peptides have been reported. Here, we performed replica exchange molecular dynamics (REMD) simulations of model peptides (exon 6, 26A-1, and 26A-2) extracted from elastin to investigate their structural features, thereby revealing the factor that influences stereoinversions. For REMD trajectories, we calculated distances between carboxyl carbon in Asp and amide nitrogen in the (n + 1) residue (C-N distances). Because bond formation between carbon and nitrogen is indispensable to the formation of a succinimide intermediate the distance between them seems to play an important role in stereoinversion...
January 10, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29331331/interaction-of-ceramides-and-tear-lipocalin
#16
Ben J Glasgow, Adil R Abduragimov
The distribution of lipids in tears is critical to their function. Lipids in human tears may retard evaporation by forming a surface barrier at the air interface. Lipids complexed with the major lipid binding protein in tears, tear lipocalin, reside in the bulk (aqueous) and may have functions unrelated to the surface. Many new lipids species have been revealed through recent mass spectrometric studies. Their association with lipid binding proteins has not been studied. Squalene, (O-acyl) omega-hydroxy fatty acids (OAHFA) and ceramides are examples...
January 10, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29329791/corrigendum-to-bcl-xl-deamidation-and-cancer-charting-the-fame-trajectories-of-legitimate-child-and-hidden-siblings-biochim-biophys-acta-1864-10-2017-1734-1745
#17
Florian Beaumatin, Mohamad El Dhaybi, Claude Bobo, Mireille Verdier, Muriel Priault
No abstract text is available yet for this article.
January 10, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29330024/nucleophosmin-1-regions-associated-with-acute-myeloid-leukemia-interact-differently-with-lipid-membranes
#18
Augusta De Santis, Sara La Manna, Irene Russo Krauss, Anna Maria Malfitano, Ettore Novellino, Luca Federici, Antonella De Cola, Adele Di Matteo, Gerardino D'Errico, Daniela Marasco
No abstract text is available yet for this article.
January 9, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29330023/unraveling-the-differential-structural-stability-and-dynamics-features-of-t7-endolysin-partially-folded-conformations
#19
Meenakshi Sharma, Dinesh Kumar, Krishna Mohan Poluri
BACKGROUND: Characterization of partially collapsed protein conformations at atomic level is a daunting task due to their inherent flexibility and conformational heterogeneity. T7 bacteriophage endolysin (T7L) is a single-domain amidase that facilitates the lysis of Gram-negative bacteria. T7L exhibits a pH-dependent structural transition from native state to partially folded (PF) conformation. In the pH range 5-3, T7L PF states display differential ANS binding characteristics. METHODS: CD, fluorescence, NMR spectroscopy and lysis assays were used to investigate the structure-stability- dynamics relationships of T7L PF conformations...
January 9, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29329987/quantitative-proteomics-in-friedreich-s-ataxia-b-lymphocytes-a-valuable-approach-to-decipher-the-biochemical-events-responsible-for-pathogenesis
#20
Lorène Télot, Elodie Rousseau, Emmanuel Lesuisse, Camille Garcia, Bastien Morlet, Thibaut Léger, Jean-Michel Camadro, Valérie Serre
Friedreich's ataxia (FRDA) represents the most frequent type of autosomal-recessively inherited ataxia and is caused by the deficiency of frataxin, a mitochondrial protein. It is known that frataxin-deficiency leads to alterations in cellular and mitochondrial iron metabolism and impacts in the cell physiology at several levels. Frataxin is thought to play a role in iron-sulfur cluster biogenesis and heme synthesis. Currently, cellular antioxidant defense is dysregulated when frataxin is deficient, which exacerbates oxidative damage in FRDA...
January 9, 2018: Biochimica et Biophysica Acta
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