1,027 results match your criteria Biochimica et biophysica acta. General subjects[Journal]


A pericellular hyaluronan matrix is required for the morphological maturation of cortical neurons.

Biochim Biophys Acta Gen Subj 2020 Jul 2:129679. Epub 2020 Jul 2.

Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa-Ku, Nagoya 464-8601, Japan; Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo 183-8509, Japan. Electronic address:

Background: Hyaluronan (HA) is a major component of the extracellular matrix (ECM) and is involved in many cellular functions. In the adult brain, HA forms macromolecular aggregates around synapses and plays important roles in neural plasticity. In contrast to the well-characterized function of HA in the adult brain, its roles in the developing brain remain largely unknown. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129679DOI Listing

Influence of cytosolic conditions on the reaction equilibrium and the reaction enthalpy of the enolase reaction accessed by calorimetry and van 't HOFF.

Biochim Biophys Acta Gen Subj 2020 Jun 28:129675. Epub 2020 Jun 28.

UFZ - Helmholtz Centre for Environmental Research, Dept. Environmental Microbiology, Permoserstr. 15, D-04318 Leipzig, Germany. Electronic address:

Background: Thermodynamic methods are finding more and more applications in systems biology, which attempts to understand cell functions mechanistically. Unfortunately, the state variables used (reaction enthalpy and Gibbs energy) do not take sufficient account of the conditions inside of cells, especially the crowding with macromolecules.

Methods: For this reason, the influence of crowding agents and various other parameters such as salt concentrations, pH and temperature on equilibrium position and reaction enthalpy of the glycolytic example reaction 9 (2-Phospoglycerate - > Phosphoenolpyruvate + HO) was investigated. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129675DOI Listing

Biometals and glycosylation in humans: Congenital disorders of glycosylation shed lights into the crucial role of manganese Golgi homeostasis.

Biochim Biophys Acta Gen Subj 2020 Jun 26:129674. Epub 2020 Jun 26.

Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France. Electronic address:

About half of the eukaryotic proteins bind biometals that participate in their structure and functions in virtually all physiological processes, including glycosylation. After reviewing the biological roles and transport mechanisms of calcium, magnesium, manganese, zinc and cobalt acting as cofactors of the metalloproteins involved in sugar metabolism and/or glycosylation, the paper will outline the pathologies resulting from a dysregulation of these metals homeostasis and more particularly Congenital Disorders of Glycosylation (CDGs) caused by ion transporter defects. Highlighting of CDGs due to defects in SLC39A8 (ZIP8) and TMEM165, two proteins transporting manganese from the extracellular space to cytosol and from cytosol to the Golgi lumen, respectively, has emphasized the importance of manganese homeostasis for glycosylation. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129674DOI Listing

Central administration of β-MSH reduces body weight in obese male Pomc mice.

Biochim Biophys Acta Gen Subj 2020 Jun 22;1864(10):129673. Epub 2020 Jun 22.

Department of Physiology, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre for Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. Electronic address:

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http://dx.doi.org/10.1016/j.bbagen.2020.129673DOI Listing

Characterization of two siderophores produced by Bacillus megaterium: A preliminary investigation into their potential as therapeutic agents.

Biochim Biophys Acta Gen Subj 2020 Jun 19;1864(10):129670. Epub 2020 Jun 19.

Institute of Pharmaceutical Science, King's College London, London SE1 9NH, United Kingdom. Electronic address:

Background: Microorganisms produce siderophores in order to scavenge iron from the environment and this study focuses on the characterization of the two siderophores secreted by Bacillus megaterium. The general biological properties and pharmacokinetics following oral application of these compounds are reported.

Methods: Under optimized culture conditions, the siderophores were harvested, purified by chromatography and identified using LC-MS and NMR. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129670DOI Listing

Coating of magnetic nanoparticles affects their interactions with model cell membranes.

Biochim Biophys Acta Gen Subj 2020 Jun 18:129671. Epub 2020 Jun 18.

Biomedical Research Foundation, Academy of Athens, Soranou Ephessiou 4, Athens 11527, Greece. Electronic address:

Background: The use of functionalized iron oxide nanoparticles of various chemical properties and architectures offers a new promising direction in gene delivery and silencing, cellular imaging and cancer imaging and treatment. The increasing applications of nanoparticles in medicine require that these engineered nanomaterials will come in contact with human cells without damaging essential tissues. Thus, efficient delivery must be achieved while minimizing cytotoxicity during passage through cell membranes to reach intracellular target compartments. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129671DOI Listing

Oxidative stress-mediated epidermal growth factor receptor activation regulates PM-induced over-secretion of pro-inflammatory mediators from human bronchial epithelial cells.

Biochim Biophys Acta Gen Subj 2020 Jun 18;1864(10):129672. Epub 2020 Jun 18.

Henan International Collaborative Laboratory for Health Effects and Intervention of Air Pollution, School of Public Health, Xinxiang Medical University, Xinxiang, Henan Province 453003, China. Electronic address:

Background: Exposure to PM has been associated with increased morbidity and mortality of lung diseases although the underlying mechanisms have not been fully uncovered. Airway inflammation is a critical event in the pathogenesis of lung diseases. This study aimed to examine the role of oxidative stress and epidermal growth factor receptor (EGFR) in PM-induced pro-inflammatory response in a human bronchial epithelial cell line, BEAS-2B. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129672DOI Listing

Dynamic alterations in serum IgG N-glycan profiles in the development of colitis-associated colon Cancer in mouse model.

Biochim Biophys Acta Gen Subj 2020 Jun 14;1864(10):129668. Epub 2020 Jun 14.

NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China. Electronic address:

Background: Alternative glycosylation of serum IgG has been shown to be closely associated with colorectal cancer (CRC). Currently, a dynamic study which can not only minimize the influence of genetic background, environment and other interfering factors during cancer development, but also focus on investigating carcinogenic characteristics of IgG glycan is lacking.

Methods: Serum IgG N-glycans were characterized at four stages of CRC development by ultra-performance liquid chromatography in a typical colitis-related CRC mouse model induced by azoxymethane-dextran sodium sulfate. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129668DOI Listing

Role of PARP-1 in mitochondrial homeostasis.

Biochim Biophys Acta Gen Subj 2020 Jun 14;1864(10):129669. Epub 2020 Jun 14.

Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India. Electronic address:

Background: Nuclear poly(ADP-ribose) polymerase-1 (PARP-1) is a well characterised protein that accounts for the majority of PARylation reactions using NAD as a substrate, regulating diverse cellular functions. In addition to its nuclear functions, several recent studies have identified localization of PARP-1 in mitochondria and emphasized its possible role in maintaining mitochondrial homeostasis. Various reports suggest that nuclear PARP-1 has been implicated in diverse mitochondria-specific communication processes. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129669DOI Listing

A computational study of effects on membrane recruitment of the polar linkers in Vitamin E derivatives.

Biochim Biophys Acta Gen Subj 2020 Jun 11;1864(10):129655. Epub 2020 Jun 11.

Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States. Electronic address:

Background: Previous studies found that Vitamin E (VE) could recruit protein kinase B (Akt1) to the membrane by targeting its unconventional lipid-binding site, which led to the dephosphorylation of Akt1 at Ser473, eventually deactivating the enzyme.

Methods: A series of VE-like compounds with varying types and lengths of the linker groups are designed to study the VE-driven membrane recruitment of Akt1 using a combined molecular docking and molecular dynamics (MD) simulation approach.

Results: We find that the linker groups with only one methylene linker and multiple hydrogen bond donors are optimal for achieving a balance between binding to the protein and partitioning into the membrane to form a stable protein-ligand-membrane ternary complex. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129655DOI Listing

The c-MET oncoprotein: Function, mechanisms of degradation and its targeting by novel anti-cancer agents.

Biochim Biophys Acta Gen Subj 2020 Jun 6:129650. Epub 2020 Jun 6.

Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, Medical Foundation Building (K25), University of Sydney, New South Wales 2006, Australia,; Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Centre for Cancer Cell Biology, Griffith University, Griffith Institute of Drug Discovery, Nathan, Brisbane, Queensland, Australia. Electronic address:

Background: The c-MET oncoprotein drives cancer progression in a variety of tumors through its signaling transduction pathways. This oncoprotein is also degraded by multiple mechanisms involving the lysosome, proteasome and cleavage by proteases. Targeting c-MET degradation pathways may result in effective therapeutic strategies. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129650DOI Listing

CDG biochemical screening: Where do we stand?

Biochim Biophys Acta Gen Subj 2020 Jun 5;1864(10):129652. Epub 2020 Jun 5.

Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France. Electronic address:

Background: Glycosylation is one of the most complex post-translational modifications of proteins and lipids, notably requiring many glycosyltransferases, glycosidases and sugar transporters encoded by about 1-2% of all human genes. Deleterious variants in any of them may result in improper protein or lipid glycosylation, thus yielding the so-called 'congenital disorders of glycosylation' or CDG.

Scope Of Review: We first review the current state of knowledge on the common blood and cellular glycoproteins used in the biochemical screening of CDG, as well as the emerging ones for an improved diagnosis. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129652DOI Listing

Computation of FRAP recovery times for linker histone - chromatin binding on the basis of Brownian dynamics simulations.

Biochim Biophys Acta Gen Subj 2020 Jun 5;1864(10):129653. Epub 2020 Jun 5.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany. Electronic address:

Background Fluorescence recovery after photobleaching (FRAP) studies can provide kinetic information about proteins in cells. Single point mutations can significantly affect the binding kinetics of proteins and result in variations in the recovery half time (t) measured in FRAP experiments. FRAP measurements of linker histone (LH) proteins in the cell nucleus have previously been reported by Brown et al. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129653DOI Listing

Non-contact microfluidic mechanical property measurements of single apoptotic bodies.

Biochim Biophys Acta Gen Subj 2020 Jun 6:129657. Epub 2020 Jun 6.

Engineering Department, University of Massachusetts Boston, Boston, MA 02125, United States of America. Electronic address:

Background: Cells exchange information by secreting micro- and nanosized extracellular vesicles (EVs), ranging from exosomes (30-100 nm) to apoptotic bodies (ABs, 1-5 μm). There is still much to understand about fundamental EV biological, physical, and chemical properties before clinical applications can be developed. EV mechanical properties have only been measured with atomic force microscopy (AFM) with its problematic adhesion and hard substrate effects. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129657DOI Listing

Molecular movie of nucleotide binding to a motor protein.

Biochim Biophys Acta Gen Subj 2020 Jun 5;1864(10):129654. Epub 2020 Jun 5.

Department of Physics, Graduate School of Science, Nagoya University, Aichi 464-8602, Japan; JST-CREST, Nagoya, Aicihi 464-8602, Japan.

Background: The SecA DEAD (Asp-Glu-Ala-Asp) motor protein uses binding and hydrolysis of adenosine triphosphate (ATP) to push secretory proteins across the plasma membrane of bacteria. The reaction coordinate of nucleotide exchange is unclear at the atomic level of detail.

Methods: We performed multiple atomistic computations of the DEAD motor domain of SecA with different occupancies of the nucleotide and magnesium ion sites, for a total of ~1. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129654DOI Listing

Rab7 of Plasmodium falciparum is involved in its retromer complex assembly near the digestive vacuole.

Biochim Biophys Acta Gen Subj 2020 Jun 5;1864(10):129656. Epub 2020 Jun 5.

Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India. Electronic address:

Background: Intracellular protein trafficking is crucial for survival of cell and proper functioning of the organelles; however, these pathways are not well studied in the malaria parasite. Its unique cellular architecture and organellar composition raise an interesting question to investigate.

Methods: The interaction of Plasmodium falciparum Rab7 (PfRab7) with vacuolar protein sorting-associated protein 26 (PfVPS26) of retromer complex was shown by coimmunoprecipitation (co-IP). Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129656DOI Listing

Characteristics of SNARE proteins are defined by distinctive properties of SNARE motifs.

Biochim Biophys Acta Gen Subj 2020 Jun 6;1864(10):129658. Epub 2020 Jun 6.

Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China. Electronic address:

Background: Syntaxin-1A and Sso1 are syntaxin family SNARE proteins engaged in synaptic vesicle fusion and yeast exocytosis. The syntaxin-1A SNARE motif can form a fusogenic SNARE complex with Sso1 partners. However, a chimera in which the SNARE motif in syntaxin-1A is introduced into Sso1 was not functional in yeast because the chimera is retained in the ER. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129658DOI Listing
June 2020
4.381 Impact Factor

Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA.

Biochim Biophys Acta Gen Subj 2020 Sep 31;1864(9):129651. Epub 2020 May 31.

Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic. Electronic address:

Background: The i-motif is a tetrameric DNA structure based on the formation of hemiprotonated cytosine-cytosine (C.C) base pairs. i-motifs are widely used in nanotechnology. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129651DOI Listing
September 2020

Inosine 5'-diphosphate, a molecular decoy rescues Nucleoside diphosphate kinase from c-MYC G-Quadruplex unfolding.

Biochim Biophys Acta Gen Subj 2020 Sep 31;1864(9):129649. Epub 2020 May 31.

Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata 700054, India. Electronic address:

Background: The transcription-inhibitory G-Quadruplex(Pu27-GQ) at c-MYC promoter is challenging to target due to structural heterogeneity. Nucleoside diphosphate kinase (NM23-H2) specifically binds and unfolds Pu27-GQ to increase c-MYC transcription. Here, we used Inosine 5'-diphosphate (IDP) to disrupt NM23-H2-Pu27-GQ interactions and arrest c-MYC transcription without compromising NM23-H2-mediated kinase properties. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129649DOI Listing
September 2020
4.381 Impact Factor

Imaging extracelluar vesicles by transmission electron microscopy: Coping with technical hurdles and morphological interpretation.

Biochim Biophys Acta Gen Subj 2020 May 30:129648. Epub 2020 May 30.

Department of Veterinary Medicine, University of Perugia, Via S. Costanzo, 4, Perugia, Italy.

Background: Extracellular vesicles (EVs) are cell-derived nanometric particles governing the complex interactions among cells through their bioactive cargo. Interest in EVs is rapidly increasing due to their extensive involvement in physiological and pathological conditions, their potential employment as diagnostic and therapeutic tools and their prospective use as bio-carriers of exogenous molecules. Given their nanometric size, transmission electron microscopy (TEM) provides significant contributions to assess EV presence and purity in a sample and to study morphological features. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129648DOI Listing

Mitochondrial research in Asia: A step for the mito-global conference.

Biochim Biophys Acta Gen Subj 2020 Sep 29;1864(9):129638. Epub 2020 May 29.

Department of Neurology, Juntendo University Graduate School of Medicine, Bunkyo, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbagen.2020.129638DOI Listing
September 2020

The fibrinogen C-terminal domain is seldom C-mannosylated but its C-mannosylation is important for the secretion of microfibril-associated glycoprotein 4.

Biochim Biophys Acta Gen Subj 2020 Sep 19;1864(9):129637. Epub 2020 May 19.

Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 223-8522, Japan. Electronic address:

Background: C-mannosylation is the one of glycosylations. Microfibril-associated glycoprotein 4 (MFAP4), an important protein for tissue homeostasis and cell adhesion, contains a consensus sequence of C-mannosylation in its fibrinogen C-terminal domain. In this study, we sought to demonstrate that fibrinogen C-terminal domain is a new substrate domain for C-mannosylation. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129637DOI Listing
September 2020

Human proline specific peptidases: A comprehensive analysis.

Biochim Biophys Acta Gen Subj 2020 Sep 17;1864(9):129636. Epub 2020 May 17.

A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.

Background: Proline specific peptidases (PSPs) are a unique group of enzymes that specifically cleave bonds formed by a proline residue. The study of PSPs is important due to their role in the maturation and degradation of peptide hormones and neuropeptides. In addition, changes in the activity of PSPs can result in pathological conditions, including various types of cancer. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129636DOI Listing
September 2020

AMPK is essential for IL-10 expression and for maintaining balance between inflammatory and cytoprotective signaling.

Biochim Biophys Acta Gen Subj 2020 Aug 11;1864(8):129631. Epub 2020 May 11.

College of Pharmacy, Yeungnam University, Gyeongsan 38541, Republic of Korea. Electronic address:

Background: AMP-activated protein kinase (AMPK) exerts its anti-inflammatory effects by suppressing redox-sensitive nuclear factor kappa B (NF-κB) and pro-inflammatory cytokines including TNF-α. However, it is unclear whether AMPK regulates anti-inflammatory cytokine expressions in the presence of oxidative stress-induced inflammation. We sought to elucidate the mechanisms whereby AMPK regulates inflammatory cytokine expressions under NADPH oxidase (NOX)-induced oxidative stress. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129631DOI Listing

O-linked N-acetylgalactosamine modification is present on the tumor suppressor p53.

Biochim Biophys Acta Gen Subj 2020 Aug 14;1864(8):129635. Epub 2020 May 14.

Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai, China. Electronic address:

Background: Mucin-type O-glycosylation (referred to as O-GalNAc glycosylation) is the most abundant O-glycosylation on membrane and secretory proteins. Recently several evidences suggest that nuclear or cytoplasmic proteins might also have O-GalNAc glycosylation. However, what nucleocytoplasmic proteins are O-GalNAc glycosylated and what the biological function of this modification in cells are still poorly understood. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129635DOI Listing
August 2020
4.381 Impact Factor

Mitochondria as targets for toxicity and metabolism research using zebrafish.

Biochim Biophys Acta Gen Subj 2020 Aug 15;1864(8):129634. Epub 2020 May 15.

Biochemistry Department, Federal University of Pernambuco - UFPE, Recife, PE, Brazil.

Background: The study of mitochondrial functions in zebrafish was initiated before the 1990s and has effectively supported many of the recent scientific advances in the functional studies of mitochondria.

Scope Of Review: This work elaborates various peculiarities and general advances in the study of mitochondria using this animal model.

Major Conclusions: The inclusion of zebrafish models in scientific research was initiated with structural studies of mitochondria. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129634DOI Listing

EcDBS1R6: A novel cationic antimicrobial peptide derived from a signal peptide sequence.

Biochim Biophys Acta Gen Subj 2020 Sep 13;1864(9):129633. Epub 2020 May 13.

S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília, DF, Brazil; Molecular Pathology Post-graduate Program, University of Brasília, Brasília, Distrito Federal, Brazil. Electronic address:

Background: Bacterial infections represent a major worldwide health problem the antimicrobial peptides (AMPs) have been considered as potential alternative agents for treating these infections. Here we demonstrated the antimicrobial activity of EcDBS1R6, a peptide derived from a signal peptide sequence of Escherichia coli that we previously turned into an AMP by making changes through the Joker algorithm.

Methods: Antimicrobial activity was measured by broth microdilution method. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129633DOI Listing
September 2020

Role of C-mannosylation in the secretion of mindin.

Biochim Biophys Acta Gen Subj 2020 Aug 19;1864(8):129632. Epub 2020 May 19.

Department of Biochemistry, School of Medicine, Wakayama Medical University, Wakayama 641-0012, Japan. Electronic address:

Background: Mindin (spondin2), a secretory protein related to neural development and immunity, is a member of thrombospondin type I repeat (TSR) superfamily proteins, and has a unique glycosylation of C-mannosylation in its structure. However, it remains unclear whether C-mannosylation plays a functional role in the biosynthesis of mindin in cells.

Methods: Protein C-mannosylation was analyzed by mass spectrometry. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129632DOI Listing

New insights into serum/extracellular thioredoxin in regulating hepatic insulin receptor activation.

Biochim Biophys Acta Gen Subj 2020 Aug 4;1864(8):129630. Epub 2020 May 4.

Medical School, University of Chinese Academy of Sciences, the Campus of Yanqi, Huai Rou, Beijing 101407, China. Electronic address:

Background: Serum thioredoxin of type-2 diabetic patients is significantly higher than that of healthy people. Pathophysiological significance is unclear.

Methods: Effects of serum/extracellular thioredoxin on phosphorylation (activation) of hepatic insulin receptor (IR) were investigated by using methods in biochemistry, cell/molecular biology and mass spectrometry. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129630DOI Listing

Matrix vesicle biomimetics harboring Annexin A5 and alkaline phosphatase bind to the native collagen matrix produced by mineralizing vascular smooth muscle cells.

Biochim Biophys Acta Gen Subj 2020 Aug 29;1864(8):129629. Epub 2020 Apr 29.

Department of Chemistry, FFCLRP-USP, University of São Paulo, Ribeirão Preto, SP, Brazil. Electronic address:

Backgound: Vascular smooth muscle cells (VSMCs) transdifferentiated ectopically trigger vascular calcifications, contributing to clinical cardiovascular disease in the aging population. AnxA5 and TNAP play a crucial role in (patho)physiological mineralization.

Methods: We performed affinity studies between DPPC and 9:1 DPPC:DPPS-proteoliposomes carrying AnxA5 and/or TNAP and different types of collagen matrix: type I, II, I + III and native collagenous extracellular matrix (ECM) produced from VSMCs with or without differentiation, to simulate ectopic calcification conditions. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129629DOI Listing

The multiple activities of BAG3 protein: Mechanisms.

Biochim Biophys Acta Gen Subj 2020 Aug 28;1864(8):129628. Epub 2020 Apr 28.

Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, SA 84081, Italy. Electronic address:

Background: BAG3 was identified as a co-chaperone of the heat shock protein (Hsp) 70, which helps, through the binding to the ATPase domain, the ADP release from the chaperone and the nucleotide cycling. By interacting with Hsp70, BAG3 modulates the activities of this chaperone, including the delivery of client proteins to proteasome. BAG3 can also carry out Hsp70- independent functions, through its interactions with other proteins involved in apoptosis, cytoskeleton dynamics and other pathways. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129628DOI Listing

Immune modulations and survival strategies of evolved hypervirulent Salmonella Typhimurium strains.

Biochim Biophys Acta Gen Subj 2020 Aug 28;1864(8):129627. Epub 2020 Apr 28.

Laboratory of Infection Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India. Electronic address:

Background: Evolving multidrug-resistance and hypervirulence in Salmonella is due to multiple host-pathogen, and non-host environmental interactions. Previously we had studied Salmonella adaptation upon repeated exposure in different in-vitro and in-vivo environmental conditions. This study deals with the mechanistic basis of hypervirulence of the passaged hypervirulent Salmonella strains reported previously. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129627DOI Listing
August 2020
4.381 Impact Factor

NDRG1 suppresses basal and hypoxia-induced autophagy at both the initiation and degradation stages and sensitizes pancreatic cancer cells to lysosomal membrane permeabilization.

Biochim Biophys Acta Gen Subj 2020 Aug 23;1864(8):129625. Epub 2020 Apr 23.

Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, Medical Foundation Building (K25), University of Sydney, Sydney, New South Wales 2006, Australia; Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Centre for Cancer Cell Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia. Electronic address:

Background: N-myc downstream regulated gene 1 (NDRG1) is an established stress-response protein. This study investigated the effects of NDRG1 on autophagic degradation and how this can be therapeutically exploited.

Methods: Cell culture, western analysis, confocal microscopy, acridine orange staining, cholesterol determination, cellular proliferation assessment and combination index (CI) estimation. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129625DOI Listing

TAT-tagging of VIP exerts positive allosteric modulation of the PAC1 receptor and enhances VIP neuroprotective effect in the MPTP mouse model of Parkinson's disease.

Biochim Biophys Acta Gen Subj 2020 Aug 23;1864(8):129626. Epub 2020 Apr 23.

Normandie Univ, UNIROUEN, Inserm, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Neuropeptides, Neuronal Death, Cell plasticity Team, Rouen, France.

Background: The cationic Arginine-rich peptide (CARP) TAT had been tagged at the C-terminal end of the vasoactive intestinal peptide (VIP) to construct VIP-TAT in order to improve traversing ability. Interestingly, it was found that TAT may bind the positive allosteric modulation (PAM) site of the N-terminal extracellular domain of neuropeptide receptor PAC1 (PAC1-EC1), imitating the C-terminus part of pituitary adenylate cyclase-activating polypeptide (PACAP) PACAP(28-38) fragment.

Methods: To test this hypothesis, we addressed the neuroprotective effects of VIP, VIP-TAT and PACAP38 in Parkinson's Disease (PD) cellular and mouse models. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129626DOI Listing

Proton transfer in the D-channel of cytochrome c oxidase modeled by a transition network approach.

Biochim Biophys Acta Gen Subj 2020 Aug 17;1864(8):129614. Epub 2020 Apr 17.

Department of Physics, Freie Universität Berlin, Arnimallee 14, 14159 Berlin, Germany. Electronic address:

Background: Determination of proton uptake pathways in Cytochrome c Oxidase is difficult due to the complexity of the system. The transition networks approach allows sampling of proton transfer pathways without predefined reaction coordinate.

Methods: Computation of the proton transfer pathways in a model of the D-channel of cytochrome c oxidase has been performed by a transition network approach that combines discrete, optimisation based and molecular dynamics based sampling. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129614DOI Listing

Profiling calcium-dependent interactions between Sorcin and intrinsically disordered regions of human proteome.

Biochim Biophys Acta Gen Subj 2020 Aug 17;1864(8):129618. Epub 2020 Apr 17.

Department of Chemistry - BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.

Background: Sorcin is a calcium sensor that exerts many calcium-related functions in the cells, e.g. it regulates calcium concentration in the cytoplasm, endoplasmic reticulum (ER) and mitochondria, by interacting with calcium pumps, exchangers and channels. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129618DOI Listing

A ring-shaped protein clusters gold nanoparticles acting as molecular scaffold for plasmonic surfaces.

Biochim Biophys Acta Gen Subj 2020 Aug 15;1864(8):129617. Epub 2020 Apr 15.

Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 Coppito, L'Aquila, Italy. Electronic address:

Background: Proteins are efficient supramolecular scaffolds to drive self-assembly of nanomaterials into regular colloidal structures suitable for several purposes, including cell imaging and drug delivery. Proteins, in particular, can bind to gold nanoparticles (AuNPs) through van der Waals and electrostatic forces as well as coordination and hydrogen bonds leading their assembly into responsive nanostructures.

Methods: Bioconjugation of alkyne Raman tag-labeled 20 nm AuNPs with the ring-shaped protein Peroxiredoxin (Prx), characterized by a symmetric homo-oligomeric circular arrangement, has been investigated by absorption spectroscopy, transmission and scanning electron microscopy. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129617DOI Listing

Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor.

Biochim Biophys Acta Gen Subj 2020 Aug 13;1864(8):129615. Epub 2020 Apr 13.

Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA. Electronic address:

Background: Ensemble docking has proven useful in drug discovery and development. It increases the hit rate by incorporating receptor flexibility into molecular docking as demonstrated on important drug targets including G-protein-coupled receptors (GPCRs). Adenosine A receptor (AAR) is a key GPCR that has been targeted for treating cardiac ischemia-reperfusion injuries, neuropathic pain and renal diseases. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261249PMC

Protein mechanics probed using simple molecular models.

Biochim Biophys Acta Gen Subj 2020 Aug 13;1864(8):129613. Epub 2020 Apr 13.

Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom. Electronic address:

Background: Single-molecule experimental techniques such as optical tweezers or atomic force microscopy are a direct probe of the mechanical unfolding/folding of individual proteins. They are also a means to investigate free energy landscapes. Protein force spectroscopy alone provides limited information; theoretical models relate measurements to thermodynamic and kinetic properties of the protein, but do not reveal atomic level information. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129613DOI Listing

Robosample: A rigid-body molecular simulation program based on robot mechanics.

Biochim Biophys Acta Gen Subj 2020 Aug 13;1864(8):129616. Epub 2020 Apr 13.

Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, Bucharest 060031, Romania. Electronic address:

Background: Compared with all-atom molecular dynamics (MD), constrained MD methods allow for larger time steps, potentially reducing computational cost. For this reason, there has been continued interest in improving constrained MD algorithms to increase configuration space sampling in molecular simulations.

Methods: Here, we introduce Robosample, a software package that implements high-performance constrained dynamics algorithms, originally developed for robotics, and applies them to simulations of biomolecular systems. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129616DOI Listing

Metabolic characterization of a paused-like pluripotent state.

Biochim Biophys Acta Gen Subj 2020 Aug 6;1864(8):129612. Epub 2020 Apr 6.

CNC-Center for Neuroscience and Cell Biology, CIBB, Azinhaga de Santa Comba, Polo 3, University of Coimbra, Coimbra, Portugal; University of Coimbra, Department of Life Sciences, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal. Electronic address:

Embryonic diapause is a conserved reproductive strategy in which development arrests at the blastocyst phase. Recently mammalian target of rapamycin (mTOR) inhibition was shown to induce diapause on mouse blastocysts and a paused-like state on mouse embryonic stem cells (mESCs). In this work, we aimed to further characterize this new paused-pluripotent state, focusing on its glycolytic and oxidative metabolic function. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129612DOI Listing

Hybrid giant lipid vesicles incorporating a PMMA-based copolymer.

Biochim Biophys Acta Gen Subj 2020 Apr 7:129611. Epub 2020 Apr 7.

Department of Earth, Environmental and Physical Sciences - DEEP Sciences - Pian dei Mantellini 44, 53100 Siena, Italy.

Background: In recent years, there has been a growing interest in the formation of copolymer-lipid hybrid self-assemblies, which allow combining and improving the main features of pure lipid-based and copolymer-based systems known for their potential applications in the biomedical field. As the most common method used to obtain giant vesicles is electroformation, most systems so far used low T polymers for their flexibility at room temperature.

Methods: Copolymers used in the hybrid vesicles have been synthesized by a modified version of the ATRP, namely the Activators ReGenerated by Electron Transfer ATRP and characterized by NMR and DSC. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129611DOI Listing

Regulatory expression of bone morphogenetic protein 6 by 2,2'-dipyridyl.

Biochim Biophys Acta Gen Subj 2020 Aug 3;1864(8):129610. Epub 2020 Apr 3.

Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan. Electronic address:

Background: Expression of hepcidin, a hormone produced by hepatocytes which negatively regulates the circulating iron levels, is known to be positively regulated by BMP6, a member of transforming growth factor (TGF)-β family. Previous studies have shown that iron status is sensed by sinusoidal endothelial cells of hepatic lamina, leading to the modulation of BMP6 expression.

Methods: ISOS-1, HUVEC, F-2, and SK-HEP1 endothelial cells were treated with either iron or 2,2'-dipyridyl (2DP), a cell-permeable iron-chelator, and expression level of Bmp6 was examined. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129610DOI Listing

Release of extracellular vesicle miR-494-3p by ARPE-19 cells with impaired mitochondria.

Biochim Biophys Acta Gen Subj 2020 Mar 30:129598. Epub 2020 Mar 30.

Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America. Electronic address:

Background: Mitochondrial function in retinal pigmented epithelial (RPE) cells and extracellular vesicle (EV) formation/release are related through the lysosomal and exocytotic pathways that process and eliminate intracellular material, including mitochondrial fragments. We propose that RPE cells with impaired mitochondria will release EVs containing mitochondrial miRNAs that reflect the diminished capacity of mitochondria within these cells.

Methods: We screened ARPE-19 cells for miRNAs that localize to the mitochondria, exhibit biological activity, and are present in EVs released by both untreated cells and cells treated with rotenone to induce mitochondrial injury. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129598DOI Listing

Modeling of pathogenic variants of mitochondrial DNA polymerase: insight into the replication defects and implication for human disease.

Biochim Biophys Acta Gen Subj 2020 Jul 29;1864(7):129608. Epub 2020 Mar 29.

Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, CP 36821 Irapuato, Guanajuato, Mexico. Electronic address:

Background: Mutations in human gene encoding the mitochondrial DNA polymerase γ (HsPolγ) are associated with a broad range of mitochondrial diseases. Here we studied the impact on DNA replication by disease variants clustered around residue HsPolγ-K1191, a residue that in several family-A DNA polymerases interacts with the 3' end of the primer.

Methods: Specifically, we examined the effect of HsPolγ carrying pathogenic variants in residues D1184, I1185, C1188, K1191, D1196, and a stop codon at residue T1199, using as a model the yeast mitochondrial DNA polymerase protein, Mip1p. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129608DOI Listing

Human importin α3 and its N-terminal truncated form, without the importin-β-binding domain, are oligomeric species with a low conformational stability in solution.

Biochim Biophys Acta Gen Subj 2020 Jul 29;1864(7):129609. Epub 2020 Mar 29.

IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain. Electronic address:

Background: Eukaryotic cells have a continuous transit of macromolecules between the cytoplasm and the nucleus. Several carrier proteins are involved in this transport. One of them is importin α, which must form a complex with importin β to accomplish its function, by domain-swapping its 60-residue-long N terminus. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129609DOI Listing

High-affinity binding and catalytic activity of His/Tyr-based sequences: Extending heme-regulatory motifs beyond CP.

Biochim Biophys Acta Gen Subj 2020 Jul 29;1864(7):129603. Epub 2020 Mar 29.

Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany. Electronic address:

Background & Motivation: Peptides and proteins can interact with heme through His, Tyr, or Cys in heme-regulatory motifs (HRMs). The Cys-Pro dipeptide is a well investigated HRM, but for His and Tyr such a distinct motif is currently unknown. In addition, many heme-peptide complexes, such as heme-amyloid β, can display a peroxidase-like activity, albeit there is little understanding of how the local primary and secondary coordination environment influences catalytic activity. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129603DOI Listing

The antimicrobial peptide Temporin L impairs E. coli cell division by interacting with FtsZ and the divisome complex.

Biochim Biophys Acta Gen Subj 2020 Jul 27;1864(7):129606. Epub 2020 Mar 27.

Department of Pharmaceutical Sciences, University of Milan, Via Venezian 21, 20133 Milan, Italy. Electronic address:

Background: The comprehension of the mechanism of action of antimicrobial peptides is fundamental for the design of new antibiotics. Studies performed looking at the interaction of peptides with bacterial cells offer a faithful picture of what really happens in nature.

Methods: In this work we focused on the interaction of the peptide Temporin L with E. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129606DOI Listing

Glycine substitution in SH3-SH2 connector of Hck tyrosine kinase causes population shift from assembled to disassembled state.

Biochim Biophys Acta Gen Subj 2020 Jul 26;1864(7):129604. Epub 2020 Mar 26.

Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, United States of America; Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, United States of America. Electronic address:

A combination of small angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations based on a coarse grained model is used to examine the effect of glycine substitutions in the short connector between the SH3 and SH2 domains of Hck, a member of the Src-family kinases. It has been shown previously that the activity of cSrc kinase is upregulated by substitution of 3 residues by glycine in the SH3-SH2 connector. Here, analysis of SAXS data indicates that the population of Hck in the disassembled state increases from 25% in the wild type kinase to 76% in the glycine mutant. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129604DOI Listing

A multi-approach analysis highlights the relevance of RPA-1 as a telomere end-binding protein (TEBP) in Leishmania amazonensis.

Biochim Biophys Acta Gen Subj 2020 Jul 25;1864(7):129607. Epub 2020 Mar 25.

Department of Chemical and Biological Sciences, São Paulo State University (UNESP) - Botucatu, SP, Brazil. Electronic address:

Background: Telomeres are chromosome end structures important in the maintenance of genome homeostasis. They are replenished by the action of telomerase and associated proteins, such as the OB (oligonucleotide/oligosaccharide-binding)-fold containing telomere-end binding proteins (TEBP) which plays an essential role in telomere maintenance and protection. The nature of TEBPs is well known in higher and some primitive eukaryotes, but it remains undetermined in trypanosomatids. Read More

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http://dx.doi.org/10.1016/j.bbagen.2020.129607DOI Listing