Nuclei of HeLa cells interactomes unravel a network of ghost proteins involved in proteins translation
Publication date: Available online 23 May 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Tristan Cardon, Michel Salzet, Julien Franck, Isabelle FournierSummaryGhost proteins are issued from alternative Open Reading Frames (ORFs) and are missing a genome annotation. Indeed, historical filters applied for the detection of putative translated ORFs led to a wrong classification of transcripts considered as non-coding although translated proteins can be detected by proteomics. This Ghost (also called Alternative) proteome was neglected, and one major issue is to identify the implication of the Ghos...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 24, 2019 Category: Biochemistry Source Type: research

Amarogentin, a secoiridoid glycoside, activates AMP- activated protein kinase (AMPK) to exert beneficial vasculo-metabolic effects
ConclusionIn conclusion, AG exerts beneficial vasculo-metabolic effects by activating AMPK.General significanceAmarogentin, a naturally occurring secoiridoid glycoside, is a promising lead for design and synthesis of novel drugs for treatment and management of dyslipidemia and cardiovascular diseases. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 22, 2019 Category: Biochemistry Source Type: research

24R,25-Dihydroxyvitamin D3 regulates breast cancer cells in vitro and in vivo
ConclusionThese results indicate that 24R,25(OH)2D3 shows promise in treatment of breast cancer by stimulating tumor apoptosis and reducing metastasis.General significance24R,25(OH)2D3 regulates breast cancer cell survival through ER-associated mechanisms similar to 24R,25(OH)2D3 effects on chondrocytes. Thus, 24R,25(OH)2D3 may modulate cell survival in other estrogen-responsive cell types, and its therapeutic potential should be investigated in ER-associated pathologies. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 22, 2019 Category: Biochemistry Source Type: research

Activity of N-acylneuraminate-9-phosphatase (NANP) is not essential for de novo sialic acid biosynthesis
ConclusionsOur data provide evidence that NANP activity is not essential for de novo sialic acid production and point towards an alternative phosphatase activity, bypassing NANP.General significanceThis report contributes to a better understanding of sialic acid biosynthesis in humans. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 21, 2019 Category: Biochemistry Source Type: research

Exploitation of glycosylation in enveloped virus pathobiology
Publication date: Available online 20 May 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Yasunori Watanabe, Thomas A. Bowden, Ian A. Wilson, Max CrispinAbstractGlycosylation is a ubiquitous post-translational modification responsible for a multitude of crucial biological roles. As obligate parasites, viruses exploit host-cell machinery to glycosylate their own proteins during replication. Viral envelope proteins from a variety of human pathogens including HIV-1, influenza virus, Lassa virus, SARS, Zika virus, dengue virus, and Ebola virus have evolved to be extensively glycosylated. These host...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 21, 2019 Category: Biochemistry Source Type: research

Anti-cancer effect of marchantin C via inducing lung cancer cellular senescence associated with less secretory phenotype
ConclusionMar-C selectively inhibited tumor growth via the induction of cancer cell senescence and had little chemotherapeutic toxicity, suggesting the potential of Mar-C as a promising anticancer agent.General significanceThis study provided evidence to identify a novelty of Mar-C that exerted antitumor activity on lung cancer through induction of senescence with limited toxicity.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 18, 2019 Category: Biochemistry Source Type: research

In situ structural biology using in-cell NMR
Publication date: Available online 16 May 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Noritaka Nishida, Yutaka Ito, Ichio ShimadaAbstractBackgroundAccumulating evidence from the experimental and computational studies indicated that the functional properties of proteins are different between in vitro and living cells, raising the necessity to examine the protein structure under the native intracellular milieu. To gain structural information of the proteins inside the living cells at an atomic resolution, in-cell NMR method has been developed for the past two decades.Scope of reviewIn this re...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 18, 2019 Category: Biochemistry Source Type: research

Roles of nucleotide substructures in the regulation of cystathionine β-synthase domain-containing pyrophosphatase
ConclusionsProtein interactions with the adenine moiety of AMP induce partial release of the internal inhibition and determine nucleotide-binding co-operativity, whereas interactions with the phosphate group potentiate the internal inhibition and decrease active-site co-operativity. The ribose moiety appears to enhance the activation effect of adenine and suppress its contribution to both types of co-operativity.General significanceOur findings demonstrate for the first time that regulation of a CBS-protein (inhibition or activation) is determined by a balance of its interactions with different chemical groups of the nucle...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 18, 2019 Category: Biochemistry Source Type: research

Phyto-inspired cyclic peptides derived from plant Pin-II type protease inhibitor reactive center loops for crop protection from insect pests
ConclusionBicyclic peptides are potent inhibitors of serine proteases in the insect midgut. They cause feeding aversion and larval growth retardation. Bi-domain cyclic peptides interact with two sites on trypsin, leading to enhanced efficacy over linear RCL peptides.General significanceBicyclic peptides mimic natural PIs by inhibiting insect proteases leading to growth reduction, thus, could be used as pest control molecules in agriculture. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 10, 2019 Category: Biochemistry Source Type: research

Diffracted X-ray tracking method for recording single-molecule protein motions
Publication date: Available online 9 May 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Hirofumi ShimizuAbstractBackgroundProteins change their conformation depending on function. Although a vast number of static pictures of proteins have been accumulated, information regarding their dynamics in function is limited. Diffracted X-ray tracking (DXT) is a good candidate to obtain the missing data.Scope of reviewA gold nanocrystal was attached to the target protein as a probe and the motion of the X-ray diffraction spots from the crystal corresponded to the motion of the target. Although it has ad...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 10, 2019 Category: Biochemistry Source Type: research

Fluorescence microscopy for visualizing single-molecule protein dynamics
Publication date: Available online 10 May 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Hiroaki YokotaAbstractBackgroundSingle-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically.Scope of reviewThis paper provides an overview of the ...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 10, 2019 Category: Biochemistry Source Type: research

Editorial Board
Publication date: July 2019Source: Biochimica et Biophysica Acta (BBA) - General Subjects, Volume 1863, Issue 7Author(s): (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 10, 2019 Category: Biochemistry Source Type: research

A conserved GXXXG motif in the transmembrane domain of CLIC proteins is essential for their cholesterol-dependant membrane interaction
Conclusion: In this study, our findings uncover the identification of a GXXXG motif in CLIC1, which likely serves as the cholesterol-binding domain, that facilitates the protein's membrane interaction and insertion. Furthermore, we were able to postulate a model by which CLIC1 can autonomously insert into membranes to form functional ion channels.General significanceMembers of the CLIC family of proteins demonstrate unusual structural and dual functional properties – as ion channels and enzymes. Elucidating how the CLIC proteins' interact with membranes, thus allowing them to switch between their soluble and membrane...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 8, 2019 Category: Biochemistry Source Type: research

Non-photochemical quenching in the cells of the carotenogenic chlorophyte Haematococcus lacustris under favorable condcition and under stress
Publication date: Available online 8 May 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): K. Chekanov, E. Schastnaya, K. Neverov, S. Leu, S. Boussiba, A. Zarka, A. SolovchenkoAbstractThe microalga Haematococcus lacustris (formerly H. pluvialis) is the richest source of the valueable pigment astaxanthin, accumulated in red aplanospores (haematocysts). In this work, we report on the photoprotective mechanisms in H. lacustris, conveying this microalga its ability to cope with a wide range of adverse conditions, with special emphasis put on non-photochemical quenching (NPQ) of the excited chlorophyl...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 8, 2019 Category: Biochemistry Source Type: research

Application of digital PCR for assessing DNA fragmentation in cytotoxicity response
ConclusionsCompared to other conventional quantitative methods, the RP fragmentation index using cellular DNA represents a valid indicator in the measurement of the degree of cell death.General significanceThe demonstrated dPCR assays can precisely assess DNA fragmentation that quantitatively reflects the degree of cytotoxicity. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 7, 2019 Category: Biochemistry Source Type: research

Nanodiamonds for bioapplications–specific targeting strategies
Publication date: Available online 7 May 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Daiki Terada, Takuya Genjo, Takuya F. Segawa, Ryuji Igarashi, Masahiro ShirakawaAbstractBackgroundNanodiamonds (NDs) provide a unique multitasking system for drug delivery and fluorescent imaging in biological environments. Owing to their quantum properties, NDs are expected to be employed as multifunctional probes in the future for the accurate visualization of biophysical parameters such as temperature and magnetic fields. However, the use of NDs for the selective targeting of the biomolecules of interest...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 7, 2019 Category: Biochemistry Source Type: research

In-cell single-molecule FRET measurements reveal three conformational state changes in RAF protein
ConclusionsCytosolic CRAF has at least three conformational states; in addition to the closed and open forms, the fully-open form was distinctly specified. Based on the results, we propose a speculative structural model for CRAF.General significanceStructural distribution and changes to proteins in live cells as a result of intracellular interactions were successfully identified. smFRET using ALEX is applicable to any other cytosolic proteins. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 7, 2019 Category: Biochemistry Source Type: research

PrfA activation in Listeria monocytogenes increases the sensitivity to class IIa bacteriocins despite impaired expression of the bacteriocin receptor
ConclusionsOur results support a model in which Man-PTS acts just as a docking molecule that brings class IIa bacteriocins to the plasma membrane. Furthermore, our results suggest that lipids play a crucial role in the mechanism of action of bacteriocins.General significanceThis is the first demonstration of the link between L. monocytogenes virulence and the bacterial sensitivity toward pediocin-like peptides.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - May 4, 2019 Category: Biochemistry Source Type: research

In vitro impact of amino acid-derived bacterial metabolites on colonocyte mitochondrial activity, oxidative stress response and DNA integrity
ConclusionsSeveral bacterial metabolites produced from amino acids displayed deleterious effects on human colonocytes, in terms of genotoxicity (HO-PAA and acetaldehyde) or cytotoxicity (PAA and phenol).General significanceThis study helps understanding the consequences of intestinal microbiota's metabolic activity on the host since amino acids fermentation can lead to the formation of compounds toxic towards colonic epithelial cells. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 27, 2019 Category: Biochemistry Source Type: research

Essential role of O-GlcNAcylation in stabilization of oncogenic factors
Publication date: Available online 26 April 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Vivek Makwana, Philip Ryan, Bhautikkumar Patel, Matt Alteen, Shailendra-Anoopkumar Dukie, David J. Vocadlo, Santosh RudrawarAbstractA reversible post-translational protein modification which involves addition of N-acetylglucosamine (GlcNAc) onto hydroxyl groups of serine and/or threonine residues which is known as O-GlcNAcylation, has emerged as a potent competitor of phosphorylation. This glycosyltransfer reaction is catalyzed by the enzyme O-linked β-N-acetylglucosamine transferase (OGT). This enz...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 27, 2019 Category: Biochemistry Source Type: research

Tumor-induced neoangiogenesis and receptor tyrosine kinases – Mechanisms and strategies for acquired resistance
Publication date: Available online 25 April 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Madiha Yunus, Patric J. Jansson, Zaklina Kovacevic, Danuta S. Kalinowski, Des R. RichardsonAbstractBackgroundAngiogenesis is essential for tumor growth, proliferation and metastasis. Tumor-related angiogenesis is complex and involves multiple signaling pathways. Controlling angiogenesis is a promising strategy for limiting cancer progression.Scope of reviewSeveral receptor tyrosine kinases influence the angiogenic response via multiple signaling molecules and pathways. Understanding the functional intera...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 26, 2019 Category: Biochemistry Source Type: research

Tauroursodeoxycholic acid attenuates cyclosporine-induced renal fibrogenesis in the mouse model
Publication date: Available online 24 April 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Jody Groenendyk, Alison Robinson, Qian Wang, Miao Hu, Jingfeng Tang, Xing-Zhen Chen, Michael Mengel, R. Todd Alexander, Luis B. Agellon, Marek MichalakAbstractChronic exposure to cyclosporine causes nephrotoxicity and organ damage. Here we show that cyclosporine nephrotoxicity in vivo is associated with the activation of the unfolded protein response (UPR) pathway to initiate tissue fibrosis. We demonstrate that cyclosporine therapy activated the IRE1α branch of the unfolded protein response (UPR) ...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 25, 2019 Category: Biochemistry Source Type: research

Delineation of crosstalk between HSP27 and MMP-2/MMP-9: A synergistic therapeutic avenue for glioblastoma management
ConclusionThe association of HSP27 with MMP-2 and MMP-9 proteins along with the identified interacting stretch has the potential to contribute towards drug development to inhibit GBM infiltration and migration.General significanceCurrent findings provide a novel therapeutic target for GBM opening a new horizon in the field of GBM management.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 25, 2019 Category: Biochemistry Source Type: research

Editorial Board
Publication date: June 2019Source: Biochimica et Biophysica Acta (BBA) - General Subjects, Volume 1863, Issue 6Author(s): (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 25, 2019 Category: Biochemistry Source Type: research

PMAP-23 triggers cell death by nitric oxide-induced redox imbalance in Escherichia coli
ConclusionOur data strongly indicates that PMAP-23 mediates apoptosis-like cell death through affecting intracellular NO homeostasis. Furthermore, our results demonstrate that DinF functioned in protection from oxidative DNA damage.General significanceThe identification of PMAP-23 antibacterial activity and mechanism provides a promising antibacterial agent, supporting the role of NO in cell death regulation.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 25, 2019 Category: Biochemistry Source Type: research

Structural insights into a novel Ca2+-independent PL-6 alginate lyase from Vibrio OU02 identify the possible subsites responsible for product distribution
In this study, we characterized a novel single-domain PL-6 alginate lyase (named AlyF). According to the biochemical analysis, AlyF possesses unique features compared with other PL-6 enzymes, including (1) a Ca2+-independent catalytic mechanism and (2) a PolyG-specific cleavage specificity that predominantly produces trisaccharides. The structures of AlyF and its complexes described here reveal the structural basis for these unique features and substrate binding mechanisms, which were further confirmed using mutagenesis. More importantly, we determined the possible subsites specifying the predominantly trisaccharide produc...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 19, 2019 Category: Biochemistry Source Type: research

Tripeptide IRW initiates differentiation in osteoblasts differentiation via the RUNX2 pathway
ConclusionsIRW, an egg-derived small bioactive peptide enhances osteoblastic activity and stimulates osteogenesis. The stimulation is primarily due to the activation of PI3K-Akt-RUNX2 pathway and its downstream effectors, accompanied by a secondary collagen synthesis pathway.General significanceOur results revealed the positive effects of tripeptide IRW on regulating osteogenesis and collagen synthesis, indicating its potential for the prevention or treatment of osteoporosis.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 19, 2019 Category: Biochemistry Source Type: research

The nanoscopic molecular pathway through human skin
ConclusionsThe results indicate that lipophilic molecules penetrate the stratum corneum via the intercellular lipids bilayers separating the corneocytes in the SC, while the more water-soluble molecules penetrate the stratum corneum via the transcellular route through the corneocytes and intercellular lipid bilayers via the polar head groups of lipid molecules in the bilayers.General significanceKnowledge of the nanoscopic molecular pathways through human skin will help understand the skin barrier function and will be of use for computational skin absorption models and transdermal drug delivery strategies. (Source: Biochim...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 17, 2019 Category: Biochemistry Source Type: research

The protein disulfide isomerase family: From proteostasis to pathogenesis
Publication date: Available online 12 April 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Motonori Matsusaki, Shingo Kanemura, Misaki Kinoshita, Young-Ho Lee, Kenji Inaba, Masaki OkumuraAbstractIn mammalian cells, nearly one-third of proteins are inserted into the endoplasmic reticulum (ER), where they undergo oxidative folding and chaperoning assisted by approximately 20 members of the protein disulfide isomerase family (PDIs). PDIs consist of multiple thioredoxin-like domains and recognize a wide variety of proteins via highly conserved interdomain flexibility. Although PDIs have been studi...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 13, 2019 Category: Biochemistry Source Type: research

Antimicrobial peptide hybrid fluorescent protein based sensor array discriminate ten most frequent clinic isolates
In conclusion, the concept is based on a solid fact that antimicrobial proteins inhibit bacterial growth at a constant minimal inhibitory concentration through intercalating into the biomembrane. The developed method has a good resolution and high-faulty tolerance rate in discriminating bacteria.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 13, 2019 Category: Biochemistry Source Type: research

Light-induced formation of NO in endothelial cells by photoactivatable NADPH analogues targeting nitric-oxide synthase
ConclusionsWe show for the first time that NT photoactivation efficiently triggers electron flow at the eNOS level and increases the basal production of NO by endothelial cells.General significanceEfficient photoactivatable NADPH analogues targeting NOS could have important implications for generating apoptosis in tumor cells or modulating NO-dependent physiological processes.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 13, 2019 Category: Biochemistry Source Type: research

An insight into the dependence of the deamination rate of human APOBEC3F on the length of single-stranded DNA, which is affected by the concentrations of APOBEC3F and single-stranded DNA
ConclusionsThe concentrations of A3F-CTD and ssDNA substrates affect the ssDNA-length-dependence of deamination rate of the A3F-CTD. This unique property of A3F is rationally interpreted on the basis of its binding characteristics with ssDNA.General significanceThe discovery of the unique property of A3F regarding the deamination rate deepens the understanding of its counteraction against HIV-1. Our strategy is applicable to investigate the other aspects of the A3 activities, such as those involved in the cancer development. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 13, 2019 Category: Biochemistry Source Type: research

Metabolic activation triggered by cAMP in MCF-7 cells generates lethal vulnerability to combined oxamate/etomoxir
ConclusionscAMP-induced metabolic changes made MCF-7 cells a preferential target of a drug combination treatment which should not affect normal cell viability.General significancecAMP is a well-recognized second messenger of the pro-inflammatory cascade. The obtained results are relevant in consideration of the crucial role played by inflammation in normal breast cell transformation and in cancer progression. Furthermore, they corroborate the idea of exploiting the metabolic changes observed in cancer cells to obtain a therapeutic advantage. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 13, 2019 Category: Biochemistry Source Type: research

Yeast Dop1 is required for glycosyltransferase retrieval from the trans-Golgi network
ConclusionsOur results indicate that Dop1 is involved in vesicular transport at the TGN, and is critical for retrieving glycosyltransferases from the TGN to the Golgi in yeast.General significanceGolgi-resident glycosyltransferases recycling from the TGN to the Golgi is dependent on Dop1 and the P4-ATPase Neo1. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 13, 2019 Category: Biochemistry Source Type: research

Tripeptide IRW initiates differentiation in osteoblasts via the RUNX2 pathway
ConclusionsIRW, an egg-derived small bioactive peptide enhances osteoblastic activity and stimulates osteogenesis. The stimulation is primarily due to the activation of PI3K-Akt-RUNX2 pathway and its downstream effectors, accompanied by a secondary collagen synthesis pathway.General significanceOur results revealed the positive effects of tripeptide IRW on regulating osteogenesis and collagen synthesis, indicating its potential for the prevention or treatment of osteoporosis.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 11, 2019 Category: Biochemistry Source Type: research

Atomistic modeling and molecular dynamics analysis of human CaV1.2 channel using external electric field and ion pulling simulations
ConclusionsOur results have provided some important mechanistic insights into the structure, dynamics and ion permeation in hCaV1.2. The significant barriers for ion permeation formed by the four phenylalanine residues at the internal gate region suggest that this site is important for channel activation. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 10, 2019 Category: Biochemistry Source Type: research

An SOD1 deficiency aggravates proteasome inhibitor bortezomib-induced testicular damage in mice
Publication date: Available online 8 April 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Takujiro Homma, Junichi FujiiAbstractProteasomes play a key role in maintaining cellular homeostasis by the proteolytic removal of proteins, including ubiquitinated proteins and/or oxidatively-damaged proteins. The proteasome inhibitor bortezomib (BTZ) has been reported to exert testicular toxicity in mice. In the current study, we treated SOD1-knockout (KO) mice with BTZ and investigated the issue of whether oxidative stress is involved in the development of testicular toxicity. The BTZ treatment signifi...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 10, 2019 Category: Biochemistry Source Type: research

Multicolor redox sensor proteins can visualize redox changes in various compartments of the living cell
Publication date: Available online 4 April 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Kazunori Sugiura, Hideaki Tanaka, Genji Kurisu, Ken-ichi Wakabayashi, Toru HisaboriAbstractChange in the intracellular redox state is a consequence of various metabolic reactions, which simultaneously regulates various physiological phenomena in cells. Monitoring the redox state in living cells is thus very important for understanding cellular physiology. Various genetically encoded fluorescent redox sensors have therefore been developed. Recently, we developed oxidation-sensitive fluorescent proteins nam...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 5, 2019 Category: Biochemistry Source Type: research

Sphingosine 1-phosphate receptor 1 regulates cell-surface localization of membrane proteins in endothelial cells
In this study, we used a combination of in vivo biotinylation and liquid chromatograph tandem mass spectrometry on three mouse models of S1pr1 expression, namely normal, knockout (KO) and high, to identify EC membrane proteins whose cell-surface expression is S1pr1-dependent. EC-specific KO of S1pr1 caused severe pulmonary vascular disruption and reduction of many membrane proteins on ECs. Using the MaxQuant software we were able to identify novel membrane targets of S1pr1, for instance, Cd105 and Plvap, by comparison with their membrane expressions among the three EC model systems. Moreover, regulation of Cd105 and Plvap ...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 5, 2019 Category: Biochemistry Source Type: research

Allosteric transitions in hemoglobin revisited
Publication date: Available online 2 April 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Naoya ShibayamaAbstractBackgroundHuman hemoglobin is an allosteric protein that exerts exquisite control over ligand binding through large-scale conformational changes. The two-state model without intermediates offers a simple qualitative description of the allosteric behavior of hemoglobin, as presented in textbooks. However, there is renewed interest in this topic due to recent experimental breakthroughs that show how hemoglobin actually undergoes conformational transitions in response to environmental ...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - April 3, 2019 Category: Biochemistry Source Type: research

Kinetics and regioselectivity of three GH62 α-L-arabinofuranosidases from plant pathogenic fungi
This study expands the limited pool of characterized GH62 Abfs particularly those from plant pathogenic fungi, and provides biochemical details and methodology to evaluate regioselectivity within this glycoside hydrolase family. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - March 30, 2019 Category: Biochemistry Source Type: research

Discovery of pyridoxal reductase activity as part of human vitamin B6 metabolism
ConclusionsWe show evidence for the presence of PL reductase activity in humans. Further studies are needed to identify the responsible protein.General significanceThis study expands the number of enzymes with a role in B6 salvage pathway. We hypothesize a protective role of PL reductase(s) by limiting the intracellular amount of free PL and PLP. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - March 28, 2019 Category: Biochemistry Source Type: research

Characterization of acetyl-CoA synthetase kinetics and ATP-binding
ConclusionsThe differences in ATP-binding could explain the broadly conserved inactivation of Acs when K609 is acetylated.General SignificanceThe results presented in this study demonstrate the importance of the selected residues in Acs ATP-binding and represent an advance in our understanding of the adenylation step of the superfamily of adenylating enzymes and of their acetylation/deacetylation regulation.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - March 28, 2019 Category: Biochemistry Source Type: research

Accelerating structural life science by paramagnetic lanthanide probe methods
We describe the recent progress of structural analysis methods exploiting paramagnetic lanthanide ions. In NMR spectroscopy, the paramagnetic effects induced by the trivalent lanthanide ions provide long-range (~40 Å) distance and angular information that can be exploited in protein structure determination, ligand screening, structure-based resonance assignment, and in-cell observation. The paramagnetic lanthanide ions can also be utilized in EPR spectroscopy, providing nanometer-scale distance measurement. These applications of the paramagnetic lanthanide probe are becoming more widespread by the use of a variety ...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - March 28, 2019 Category: Biochemistry Source Type: research

Microsystem for the single molecule analysis of membrane transport proteins
Publication date: Available online 26 March 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Rikiya WatanabeAbstractMicro-chamber arrays enable highly sensitive and quantitative bioassays at the single-molecule level. Accordingly, they are widely used for ultra-sensitive biomedical applications, e.g., digital PCR and digital ELISA. However, the versatility of micro-chambers is generally limited to reactions in aqueous solutions, although various functions of membrane proteins are extremely important. To address this issue, microsystems using arrayed micro-sized chambers sealed with lipid bilayer...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - March 28, 2019 Category: Biochemistry Source Type: research

The cell resealing technique for manipulating, visualizing, and elucidating molecular functions in living cells
Publication date: Available online 23 March 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Rina Kunishige, Fumi Kano, Masayuki MurataAbstractBackgroundCell-based assays are essential for analyzing molecular functions and spatiotemporal information. The cell resealing technique, in which pore-forming toxins are used to permeabilize cell membranes, enables the delivery of various membrane-impermeable molecules inside cells.Scope of reviewWe review the basics of the resealed cell system, including optimized protocols, assessment of cellular damage, and recovery following permeabilization of the m...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - March 24, 2019 Category: Biochemistry Source Type: research

O-GlcNAcylation disrupts STRA6-retinol signals in kidneys of diabetes
ConclusionsO-GlcNAcylation significantly modified STRA6 and RALDH1, suppressed RBP4 binding activity, and disrupted retinol signals in the kidney of diabetes.General significanceThis study first indicates that STRA6-retinol signals were directly disrupted by O-GlcNAcylation in diabetic kidney. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - March 22, 2019 Category: Biochemistry Source Type: research

Editorial Board
Publication date: May 2019Source: Biochimica et Biophysica Acta (BBA) - General Subjects, Volume 1863, Issue 5Author(s): (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - March 22, 2019 Category: Biochemistry Source Type: research

Structure and dynamics of Trichoderma harzianum Cel7B suggest molecular architecture adaptations required for a wide spectrum of activities on plant cell wall polysaccharides
Publication date: Available online 19 March 2019Source: Biochimica et Biophysica Acta (BBA) - General SubjectsAuthor(s): Milton T. Sonoda, Andre S. Godoy, Vanessa O.A. Pellegrini, Marco A.S. Kadowaki, Alessandro S. Nascimento, Igor PolikarpovAbstractCellulases from glycoside hydrolase family 7 (GH7) play crucial roles in plant lignocellulose deconstruction by fungi, but structural information available for GH7 fungal endoglucanases is limited when compared to the number of known sequences in the family. Here, we report the X-ray structure of the glycosylated catalytic domain (CD) of Trichoderma harzianum endoglucanase, ThC...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - March 19, 2019 Category: Biochemistry Source Type: research

High-speed near-field fluorescence microscopy combined with high-speed atomic force microscopy for biological studies
ConclusionsThis study materialized simultaneous tip-enhanced TIRFM/HS-AFM and HS-SNOM/HS-AFM imaging at high spatiotemporal resolution. Although some issues remain to be solved in the future, these correlative microscopy methods have a potential to increase the versatility of HS-AFM in biological research.General significanceWe achieved an imaging rate of ~3 s/frame for SNOM imaging, more than 100-times higher than the typical SNOM imaging rate. We also demonstrated ~39 nm resolution in HS-SNOM imaging of fluorescently labeled DNA in solution. (Source: Biochimica et Biophysica Acta (BBA) General Subjects)
Source: Biochimica et Biophysica Acta (BBA) General Subjects - March 18, 2019 Category: Biochemistry Source Type: research