LibME-automatic extraction of 3D ligand-binding motifs for mechanistic analysis of protein-ligand recognition.

abstract：:Heterocyst-forming cyanobacteria grow as filaments that can be hundreds of cells long. Proteinaceous septal junctions provide cell-cell binding and communication functions in the filament. In Anabaena sp. strain PCC 7120, the SepJ protein is important for the formation of septal junctions. SepJ consists of integral me...

journal_title：FEBS open bio

authors： Ramos-León F,Mariscal V,Battchikova N,Aro EM,Flores E

更新日期：2017-08-30 00:00:00

abstract：:A local tissue-specific renin-angiotensin system (local RAS) has been identified in many organs. However, no report has described the role of a local RAS in the hypertrophic differentiation of chondrocytes. To examine the role of a local RAS in the hypertrophic differentiation, we activated angiotensin II type 1 recep...

journal_title：FEBS open bio

authors： Tsukamoto I,Inoue S,Teramura T,Takehara T,Ohtani K,Akagi M

更新日期：2013-07-04 00:00:00

abstract：:An imbalance of branched-chain amino acids (BCAAs) in the brain may result in neuropathological conditions, such as autism spectrum disorders. The L-type amino acid transporter 1 (LAT1), encoded by the solute carrier transporter 7a5 (Slc7a5) gene, is critical for maintaining normal levels of BCAAs in the brain. Howeve...

journal_title：FEBS open bio

authors： Onishi Y,Hiraiwa M,Kamada H,Iezaki T,Yamada T,Kaneda K,Hinoi E

更新日期：2019-01-07 00:00:00

abstract：:In brain cells, glutamine transporters are vital to monitor and control the levels of glutamate and GABA. There are 11 members of the SLC38 family of amino acid transporters of which eight have been functionally characterized. Here, we report the first histological and functional characterization of the previously orp...

journal_title：FEBS open bio

authors： Hellsten SV,Hägglund MG,Eriksson MM,Fredriksson R

更新日期：2017-04-26 00:00:00

abstract：:Sorafenib is an inhibitor of a variety of tyrosine kinase receptors used to treat various cancers including hepatocellular, renal cell and thyroid carcinoma. It has been shown to change various targets associated with osteosarcoma, but the detailed mechanism remains unclear. In order to identify key genes, enriched pa...

journal_title：FEBS open bio

authors： Dai Z,Tang H,Pan Y,Chen J,Li Y,Zhu J

更新日期：2018-04-24 00:00:00

abstract：:As a small fruit rich in anthocyanins, blueberry (Vaccinium corymbosum × angustifolium) has become a focus of research in recent years for identifying genes related to anthocyanin transport and stress resistance mechanisms based on transcriptome sequencing. However, the lack of validated, stably expressed reference ge...

journal_title：FEBS open bio

authors： Deng Y,Li Y,Sun H

更新日期：2020-08-01 00:00:00

abstract：:IL-1 family cytokines act as apical initiators of inflammation in many settings and can promote the production of a battery of inflammatory cytokines, chemokines and other inflammatory mediators in diverse cell types. IL-36α, IL-36β and IL-36γ, which belong to the extended IL-1 family, have been implicated as key init...

journal_title：FEBS open bio

authors： Sullivan GP,Davidovich PB,Sura-Trueba S,Belotcerkovskaya E,Henry CM,Clancy DM,Zinoveva A,Mametnabiev T,Garabadzhiu AV,Martin SJ

更新日期：2018-03-25 00:00:00

abstract：:PSMD9 (Proteasome Macropain non-ATPase subunit 9), a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interac...

journal_title：FEBS open bio

authors： Sangith N,Srinivasaraghavan K,Sahu I,Desai A,Medipally S,Somavarappu AK,Verma C,Venkatraman P

更新日期：2014-06-06 00:00:00

abstract：:Microorganisms or LPS (lipopolysaccharide), an outer membrane component of Gram-negative bacteria, can induce a systemic inflammatory response that leads to sepsis, multiple organ dysfunction, and mortality. Here, we investigated the role of cyclophilin D (CypD)-dependent mitochondrial permeability transition (mPT) in...

journal_title：FEBS open bio

authors： Veres B,Eros K,Antus C,Kalman N,Fonai F,Jakus PB,Boros E,Hegedus Z,Nagy I,Tretter L,Gallyas F Jr,Sumegi B

更新日期：2021-01-20 00:00:00

abstract：:The A/B domains of nuclear receptors such as thyroid receptor α (TRα) are considered to be conformationally flexible and can potentially adopt multiple structural conformations. We used intrinsic tryptophan fluorescence quenching and circular dichroism spectroscopy to characterize the unfolding of this A/B domain upon...

journal_title：FEBS open bio

authors： Fernandez EJ,Gahlot V,Rodriguez C,Amburn J

更新日期：2017-05-15 00:00:00

abstract：:Despite significant advances in understanding of the causes of and treatment of myocardial infarction (MI) in recent years, morbidity and mortality is still high. The aim of this study was to identify miRNA and genes potentially associated with MI. mRNA and miRNA expression datasets were downloaded from the Gene Expre...

journal_title：FEBS open bio

authors： Wu K,Zhao Q,Li Z,Li N,Xiao Q,Li X,Zhao Q

更新日期：2018-04-19 00:00:00

abstract：:Synthetic biology circuits are often constructed with multiple gene expression units assembled in close proximity, and they can be used to perform complex functions in embryonic stem cells (ESCs). However, mutual interference between transcriptional units has not been well studied in mouse ESCs. To assess the efficien...

journal_title：FEBS open bio

authors： Lu XB,Guo YH,Huang W

更新日期：2020-04-01 00:00:00

abstract：:The vertebrate egg coat, including mammalian zona pellucida, is an oocyte-specific extracellular matrix comprising two to six zona pellucida (ZP) glycoproteins. The egg coat plays important roles in fertilization, especially in species-specific interactions with sperm to induce the sperm acrosome reaction and to form ...

journal_title：FEBS open bio

authors： Okumura H,Sato T,Sakuma R,Fukushima H,Matsuda T,Ujita M

更新日期：2015-05-27 00:00:00

abstract：:A plant-derived Enterococcus mundtii 15-1A, that has been previously isolated from Brassica rapa L. subsp. nipposinica (L.H. Bailey) Hanelt var. linearifolia by our group, possesses two kinds of l-lactate dehydrogenase (l-LDH): LDH-1 and LDH-2. LDH-1 was activated under low concentration of fluctose-1,6-bisphosphate (...

journal_title：FEBS open bio

authors： Matoba Y,Miyasako M,Matsuo K,Oda K,Noda M,Higashikawa F,Kumagai T,Sugiyama M

更新日期：2014-09-06 00:00:00

abstract：:Inovirus XacF1 (7325 nucleotides) is integrated into the genome of Xanthomonas citri pv. citri (Xcc) strains at the host dif site (attB) by the host XerC/D recombination system. The XacF1 attP sequence is located within the coding region of ORF12, a possible phage regulator. After integration, this open reading frame ...

journal_title：FEBS open bio

authors： Ahmad AA,Kawabe M,Askora A,Kawasaki T,Fujie M,Yamada T

更新日期：2017-09-19 00:00:00

abstract：:Lactobionic acid (O-β-galactosyl-(1-4)-gluconic acid) (LBA) is a high-value lactose derivative, produced via oxidation of the reducing terminal of lactose. LBA can be produced by fermentation using certain microorganisms, although subsequent purification is challenging. Therefore, we have attempted to identify an enzy...

journal_title：FEBS open bio

authors： Lin SF,Li CK,Chung YP

更新日期：2019-01-16 00:00:00

abstract：:In this study, we showed that cyanocobalamin dodecylamine, a ribose 5'-carbamate derivative of cyanocobalamin, was absorbed and accumulated to significant levels by Caenorhabditis elegans and was not further metabolized. The levels of methylmalonic acid and homocysteine, which serve as indicators of cobalamin deficien...

journal_title：FEBS open bio

authors： Bito T,Yabuta Y,Ichiyanagi T,Kawano T,Watanabe F

更新日期：2014-08-01 00:00:00

abstract：:Human type 2 diabetes is associated with β-cell apoptosis, and human islets from diabetic donors are ∼80% deficient in PAK1 protein. Toward addressing linkage of PAK1 to β-cell survival, PAK1-siRNA targeted MIN6 pancreatic β-cells were found to exhibit increased caspase-3 cleavage, cytosolic cytochrome-C and the pro-a...

journal_title：FEBS open bio

authors： Wang Z,Thurmond DC

更新日期：2012-09-08 00:00:00

abstract：:Shiga toxin (Stx) causes fatal systemic complications. Stx induces apoptosis, but the mechanism of which is unclear. We report that Stx induced rapid reduction of short-lived anti-apoptotic proteins followed by activation of caspase 9 and the progression of apoptosis. Proteasome inhibitors prevented the reduction of a...

journal_title：FEBS open bio

authors： Hattori T,Watanabe-Takahashi M,Ohoka N,Hamabata T,Furukawa K,Nishikawa K,Naito M

更新日期：2015-06-12 00:00:00

abstract：:Adult T-cell leukemia/lymphoma (ATL), an aggressive T-cell malignancy that develops after long-term infection with human T-cell leukemia virus (HTLV-1), requires new treatments. Drug repositioning, reuse of a drug previously approved for the treatment of another condition to treat ATL, offers the possibility of reduce...

journal_title：FEBS open bio

authors： Kozako T,Soeda S,Yoshimitsu M,Arima N,Kuroki A,Hirata S,Tanaka H,Imakyure O,Tone N,Honda S,Soeda S

更新日期：2016-04-13 00:00:00

abstract：:Understanding the role of specific amino acid residues in the molecular mechanism of a protein's function is one of the most challenging problems in modern biology. A systematic bioinformatic analysis of protein families and superfamilies can help in the study of structure-function relationships and in the design of i...

journal_title：FEBS open bio

authors： Fesko K,Suplatov D,Švedas V

更新日期：2018-05-21 00:00:00

abstract：:Receptor activator of nuclear factor-κB ligand (RANKL) is required for initiation of osteoclastogenesis, with the signaling pathway including the NF-kB, c-Fos, and nuclear factor of activated T cells, cytoplasmic 1 (NFATc1) transcription factors. Because NFATc1 expression is autoamplified, we investigated the molecula...

journal_title：FEBS open bio

authors： Park KL,Oh DG,Kim YO,Song KS,Ahn DW

更新日期：2018-09-10 00:00:00

abstract：:The identification of biomarkers for early diagnosis of Parkinson's disease (PD) prior to the onset of symptoms may improve the effectiveness of therapy. To identify potential biomarkers, we downloaded microarray datasets of PD from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between PD...

journal_title：FEBS open bio

authors： Jiang F,Wu Q,Sun S,Bi G,Guo L

更新日期：2019-08-01 00:00:00

abstract：:Cisplatin-based chemotherapy is the standard treatment of choice for head and neck squamous cell carcinoma (HNSCC). The efficiency of platinum-based therapies is directly influenced by the development of tumor resistance. Multiple signaling pathways have been linked to tumor resistance, including activation of nuclear...

journal_title：FEBS open bio

authors： Almeida LO,Abrahao AC,Rosselli-Murai LK,Giudice FS,Zagni C,Leopoldino AM,Squarize CH,Castilho RM

更新日期：2013-12-30 00:00:00

abstract：:Fluorine is a bone-seeking element ubiquitously present in the environment and widely used in many oral hygiene products. In humans, excessive intake of fluoride may cause dental and skeletal fluorosis. However, endemic fluorosis does not appear to develop in a proportion of individuals exposed to the same levels of f...

journal_title：FEBS open bio

authors： Ran S,Sun N,Liu Y,Zhang W,Li Y,Wei L,Wang J,Liu B

更新日期：2017-06-05 00:00:00

abstract：:The pathogenic bacteria Streptococcus pyogenes can cause an array of diseases in humans, including moderate infections such as pharyngitis (strep throat) as well as life threatening conditions such as necrotizing fasciitis and puerperal fever. The antigen I/II family proteins are cell wall anchored adhesin proteins fo...

journal_title：FEBS open bio

authors： Hall M,Nylander S,Jenkinson HF,Persson K

更新日期：2014-03-12 00:00:00

abstract：:The extreme halophile Halococcus morrhuae (ATCC® 17082) contains a 108-nucleotide insertion in its 5S rRNA. Large rRNA expansions in Archaea are rare. This one almost doubles the length of the 5S rRNA. In order to understand how such an insertion is accommodated in the ribosome, we obtained a cryo-electron microscopy ...

journal_title：FEBS open bio

authors： Tirumalai MR,Kaelber JT,Park DR,Tran Q,Fox GE

更新日期：2020-10-01 00:00:00

abstract：:Glutathione transferases (GSTs) are involved in many processes in plant biochemistry, with their best characterised role being the detoxification of xenobiotics through their conjugation with glutathione. GSTs have also been implicated in noncatalytic roles, including the binding and transport of small heterocyclic li...

journal_title：FEBS open bio

authors： Ahmad L,Rylott EL,Bruce NC,Edwards R,Grogan G

更新日期：2016-12-22 00:00:00

abstract：:Photodynamic therapy is an advanced method of treating cancer and various benign diseases, including infections. It uses light-activated molecules [photosensitizers (PSs)] to generate reactive oxygen species (ROS) when irradiated with light of a specific wavelength. This study examined the photophysical and photosensi...

journal_title：FEBS open bio

authors： Kostryukova LV,Prozorovskiy VN,Medvedeva NV,Ipatova OM

更新日期：2018-01-02 00:00:00

abstract：:RAC3 is a coactivator of glucocorticoid receptor and nuclear factor-κB (NF-κB) that is usually over-expressed in tumors and which also has important functions in the immune system. We investigated the role of the inflammatory response in the control of RAC3 expression levels in vivo and in vitro. We found that inflamm...

journal_title：FEBS open bio

authors： Alvarado CV,Rubio MF,Fernández Larrosa PN,Panelo LC,Azurmendi PJ,Ruiz Grecco M,Martínez-Nöel GA,Costas MA

更新日期：2014-05-02 00:00:00