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https://www.readbyqxmd.com/read/28088760/usp15-regulates-dynamic-protein-protein-interactions-of-the-spliceosome-through-deubiquitination-of-prp31
#1
Tanuza Das, Joon Kyu Park, Jinyoung Park, Eunji Kim, Michael Rape, Eunice EunKyeong Kim, Eun Joo Song
Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified with K63-linked ubiquitin chains by the PRP19 complex and deubiquitinated by USP15 and its substrate targeting factor SART3. USP15(SART3) makes a complex with USP4 and this ternary complex serves as a platform to deubiquitinate PRP31 and PRP3...
January 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28088758/c5-substituents-of-uridines-and-2-thiouridines-present-at-the-wobble-position-of-trna-determine-the-formation-of-their-keto-enol-or-zwitterionic-forms-a-factor-important-for-accuracy-of-reading-of-guanosine-at-the-3-end-of-the-mrna-codons
#2
Elzbieta Sochacka, Elzbieta Lodyga-Chruscinska, Justyna Pawlak, Marek Cypryk, Paulina Bartos, Katarzyna Ebenryter-Olbinska, Grazyna Leszczynska, Barbara Nawrot
Modified nucleosides present in the wobble position of the tRNA anticodons regulate protein translation through tuning the reading of mRNA codons. Among 40 of such nucleosides, there are modified uridines containing either a sulfur atom at the C2 position and/or a substituent at the C5 position of the nucleobase ring. It is already evidenced that tRNAs with 2-thiouridines at the wobble position preferentially read NNA codons, while the reading mode of the NNG codons by R5U/R5S2U-containing anticodons is still elusive...
January 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28088612/alterations-in-cytokine-gene-expression-profile-in-colon-mucosa-of-inflammatory-bowel-disease-patients-on-different-therapeutic-regimens
#3
Tsvetelina Velikova, Dobroslav Kyurkchiev, Zoya Spassova, Iliya Karakolev, Ekaterina Ivanova-Todorova, Iskra Altankova, Spaska Stanilova
Inflammatory bowel disease (IBD) is assumed to be caused by genetic and environmental factors that interact together in promoting intestinal immune dysregulation where cytokines have validated role. However, the underlying intimate mechanisms in the human IBD involving cytokines still needs to be supplemented especially in the clinical context. The aim of this study was to investigate the expression of some inflammatory and regulatory cytokines (IL-17A, IL-23, IL-6, TGFβ1, and IL-10) as well as of the transcription factor FoxP3 in mucosal samples of IBD and non-IBD patients...
January 12, 2017: Cytokine
https://www.readbyqxmd.com/read/28088582/ripk1-protects-hepatocytes-from-kupffer-cells-mediated-tnf-induced-apoptosis-in-mouse-models-of-pamp-induced-hepatitis
#4
Aveline Filliol, Claire Piquet-Pellorce, Céline Raguénès-Nicol, Sarah Dion, Muhammad Farooq, Catherine Lucas-Clerc, Peter Vandenabeele, Mathieu J M Bertrand, Jacques Le Seyec, Michel Samson
BACKGROUND & AIMS: The severity of liver diseases is exacerbated by the death of hepatocytes, which can be induced by the sensing of Pathogen Associated Molecular Patterns (PAMPs) derived from the gut microbiota. The molecular mechanisms regulating these cell death pathways are poorly documented. In this study, we investigated the role of the Receptor Interacting Protein Kinase 1 (RIPK1), a protein known to regulate cell fate decisions, in the death of hepatocytes using two in vivo models of PAMP-induced hepatitis...
January 11, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28088539/the-dna-damage-response-of-c-elegans-affected-by-gravity-sensing-and-radiosensitivity-during-the-shenzhou-8-spaceflight
#5
Ying Gao, Dan Xu, Lei Zhao, Yeqing Sun
Space radiation and microgravity are recognized as primary and inevitable risk factors for humans traveling in space, but the reports regarding their synergistic effects remain inconclusive and vary across studies due to differences in the environmental conditions and intrinsic biological sensitivity. Thus, we studied the synergistic effects on transcriptional changes in the global genome and DNA damage response (DDR) by using dys-1 mutant and ced-1 mutant of C. elegans, which respectively presented microgravity-insensitivity and radiosensitivity when exposure to spaceflight condition (SF) and space radiation (SR)...
January 7, 2017: Mutation Research
https://www.readbyqxmd.com/read/28088516/structural-study-of-the-effects-of-mutations-in-proteins-to-identify-the-molecular-basis-of-the-loss-of-local-structural-fluidity-leading-to-the-onset-of-autoimmune-diseases
#6
Ananya Ali, Semanti Ghosh, Angshuman Bagchi
Protein-Protein Interactions (PPIs) are crucial in most of the biological processes and PPI dysfunctions are known to be associated with the onsets of various diseases. One of such diseases is the auto-immune disease. Auto-immune diseases are one among the less studied group of diseases with very high mortality rates. Thus, we tried to correlate the appearances of mutations with their probable biochemical basis of the molecular mechanisms leading to the onset of the disease phenotypes. We compared the effects of the Single Amino Acid Variants (SAVs) in the wild type and mutated proteins to identify any structural deformities that might lead to altered PPIs leading ultimately to disease onset...
January 11, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28088481/saxs-structural-studies-of-dps-from-deinococcus-radiodurans-highlights-the-conformation-of-the-mobile-n-terminal-extensions
#7
Sandra P Santos, Maxime G Cuypers, Adam Round, Stephanie Finet, Theyencheri Narayanan, Edward P Mitchell, Célia V Romão
The radiation resistant bacterium Deinococcus radiodurans contains two DNA binding proteins from starved cells (Dps): Dps1 (DR2263) and Dps2 (DRB0092). These are suggested to play a role in DNA interaction, manganese and iron storage. The proteins assemble as a conserved dodecameric structure with structurally uncharacterized N-terminal extensions. In the case of DrDps1 these extensions have been proposed to be involved in DNA interactions, while in DrDps2 their function has yet to be established. The reported data reveals the relative position of the N-terminal extensions to the dodecameric sphere in solution for both Dps...
January 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28088472/cholesterol-and-ergosterol-affect-the-activity-of-staphylococcus-aureus-antibiotic-efflux-pumps
#8
S R Tintino, C D M Oliveira-Tintino, F F Campina, M S Costa, R P Cruz, R L S Pereira, J C Andrade, E O Sousa, J P Siqueira-Junior, H D M Coutinho, T C Leal-Balbino, V Q Balbino
The aim of this study is to evaluate the effect of ergosterol on steroids and cholesterol efflux pumps in multidrug resistant strains of S. aureus. Were used RN4220 harboring plasmid pUL5054, which carries the gene encoding the MsrA macrolide efflux protein; and IS-58, which possesses the TetK tetracycline efflux protein; 1199B resists hydrophilic fluoroquinolones via a NorA-mediated mechanism and wild strain 1199B. The Minimal Inhibitory Concentration (MIC) was determined and the evaluation of possible inhibition of efflux pumps by reduction of MIC...
January 11, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28088356/advancing-the-prediction-accuracy-of-protein-protein-interactions-by-utilizing-evolutionary-information-from-position-specific-scoring-matrix-and-ensemble-classifier
#9
Lei Wang, Zhu-Hong You, Shi-Xiong Xia, Feng Liu, Xing Chen, Xin Yan, Yong Zhou
Protein-Protein Interactions (PPIs) are essential to most biological processes and play a critical role in most cellular functions. With the development of high-throughput biological techniques and in silico methods, a large number of PPI data have been generated for various organisms, but many problems remain unsolved. These factors promoted the development of the in silico methods based on machine learning to predict PPIs. In this study, we propose a novel method by combining ensemble Rotation Forest (RF) classifier and Discrete Cosine Transform (DCT) algorithm to predict the interactions among proteins...
January 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28088302/the-cyp79a1-catalyzed-conversion-of-tyrosine-to-e-p-hydroxyphenylacetaldoxime-unravelled-using-an-improved-method-for-homology-modeling
#10
Dario Vazquez-Albacete, Marco Montefiori, Stefan Kol, Mohammed Saddik Motawia, Birger Lindberg Møller, Lars Olsen, Morten H H Nørholm
The vast diversity and membrane-bound nature of plant P450s makes it challenging to study the structural characteristics of this class of enzymes especially with respect to accurate intermolecular enzyme-substrate interactions. To address this problem we here apply a modified hybrid structure strategy for homology modeling of plant P450s. This allows for structural elucidation based on conserved motifs in the protein sequence and secondary structure predictions. We modeled the well-studied Sorghum bicolor cytochrome P450 CYP79A1 catalyzing the first step in the biosynthesis of the cyanogenic glucoside dhurrin...
January 11, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28088165/genomic-characterization-of-ensifer-aridi-a-proposed-new-species-of-nitrogen-fixing-rhizobium-recovered-from-asian-african-and-american-deserts
#11
Antoine Le Quéré, Nisha Tak, Hukam Singh Gehlot, Celine Lavire, Thibault Meyer, David Chapulliot, Sonam Rathi, Ilham Sakrouhi, Guadalupe Rocha, Marine Rohmer, Dany Severac, Abdelkarim Filali-Maltouf, Jose-Antonio Munive
BACKGROUND: Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. RESULTS: Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced...
January 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28088146/photoinduced-c-i-bond-homolysis-of-5-iodouracil-a-singlet-predissociation-pathway
#12
Xiaojuan Dai, Di Song, Kunhui Liu, Hongmei Su
5-Iodouracil (5-IU) can be integrated into DNA and acts as a UV sensitive chromophore suitable for probing DNA structure and DNA-protein interactions based on the photochemical reactions of 5-IU. Here, we perform joint studies of time-resolved Fourier transform infrared (TR-FTIR) spectroscopy and ab initio calculations to examine the state-specific photochemical reaction mechanisms of the 5-IU. The fact that uracil (U) is observed in TR-FTIR spectra after 266 nm irradiation of 5-IU in acetonitrile and ascribed to the product of hydrogen abstraction by the uracil-5-yl radical (U·) provides experimental evidence for the C-I bond homolysis of 5-IU...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088132/expression-and-secretion-of-cyan-fluorescent-protein-cfp-in-b-subtilis-using-the-chitinase-promoter-from-bacillus-pumilus-sg2
#13
Abbas Shali, Garshasb Rigi, Majid Pornour, Gholamreza Ahmadian
Background: Improved cyan fluorescent protein (ICFP) is a monochromic, green fluorescent protein (GFP) derivative produced by Aequorea macrodactyla in a process similar to GFP. This protein has strong absorption spectra at wavelengths 426-446 nm. ICFP can be used in cell, organelle or intracellular protein labeling, investigating the protein-protein interactions as well as assessing the promoter activities. Methods: In our previous study, the promoters of two chitinases (ChiS and ChiL) from Bacillus pumilus SG2 were assessed in B...
15, 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28088083/specificity-and-stability-of-transient-protein-protein-interactions
#14
REVIEW
Sneha Vishwanath, Anshul Sukhwal, Ramanathan Sowdhamini, Narayanaswamy Srinivasan
Remarkable features that are achieved in a protein-protein complex to precise levels are stability and specificity. Deviation from the normal levels of specificity and stability, which is often caused by mutations, could result in disease conditions. Chemical nature, 3-D arrangement and dynamics of interface residues code for both specificity and stability. This article reviews roles of interfacial residues in transient protein-protein complexes. It is proposed that aside from hotspot residues conferring stability to the complex, a small set of 'rigid' residues at the interface that maintain conformation between complexed and uncomplexed forms, play a major role in conferring specificity...
January 11, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28088061/galectins-emerging-regulatory-checkpoints-linking-tumor-immunity-and-angiogenesis
#15
REVIEW
Santiago P Méndez-Huergo, Ada G Blidner, Gabriel A Rabinovich
Immune checkpoints, a plethora of inhibitory pathways aimed at maintaining immune cell homeostasis, may be co-opted by cancer cells to evade immune destruction. Therapies targeting immune checkpoints have reached a momentum yielding significant clinical benefits in patients with various malignancies by unleashing anti-tumor immunity. Galectins, a family of glycan-binding proteins, have emerged as novel regulatory checkpoints that promote immune evasive programs by inducing T-cell exhaustion, limiting T-cell survival, favoring expansion of regulatory T cells, de-activating natural killer cells and polarizing myeloid cells toward an immunosuppressive phenotype...
January 11, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28088012/new-4-4-chlorophenyl-2-2-6-2%C3%A2-terpyridine-ruthenium-ii-complexes-synthesis-characterization-interaction-with-dna-bsa-and-cytotoxicity-studies
#16
Milan M Milutinović, Ana Rilak, Ioannis Bratsos, Olivera Klisurić, Milan Vraneš, Nevenka Gligorijević, Siniša Radulović, Živadin D Bugarčić
In this study, we have developed a series of new monofunctional Ru(II) complexes of the general formula mer-[Ru(Cl-Ph-tpy)(N-N)Cl]Cl in which Cl-Ph-tpy is 4'-(4-chlorophenyl)-2,2':6',2″-terpyridine, N-N is a bidentate chelating ligand (1,2-diaminoethane (en, 1), 1,2-diaminocyclohexane (dach, 2) or 2,2'-bipyridine (bpy, 3)). All complexes were fully characterized by elemental analysis and spectroscopic techniques (IR, UV-Vis, 1D and 2D NMR). Their chemical behavior in aqueous solution was studied by UV-Vis and NMR spectroscopy showing that all compounds are relatively labile leading to the formation of the corresponding aqua species 1aq-3aq...
October 14, 2016: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28087981/humanized-chondroitinase-abc-sensitizes-glioblastoma-cells-to-temozolomide
#17
Alena Cristina Jaime-Ramirez, Nina Dmitrieva, Ji Young Yoo, Yeshavanth Banasavadi-Siddegowda, Jianying Zhang, Theresa Relation, Chelsea Bolyard-Blessing, Jeffrey Wojton, Balveen Kaur
INTRODUCTION: Malignant gliomas (GBMs) are extremely aggressive and have a median survival of approximately 15 months. Current treatment modalities, which include surgical resection, radiation and chemotherapy, have done little to prolong the lives of GBM patients. Chondroitin sulfate proteoglycans (CSPG) are critical for cell-cell and cell-extra cellular matrix (ECM) interactions and are implicated in glioma growth and invasion. Chondroitinase (Chase) ABC is a bacterial enzyme that cleaves chondroitin sulfate disaccharide chains from CSPGs in the tumor ECM...
January 14, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28087830/recognition-of-the-magnaporthe-oryzae-effector-avr-pia-by-the-decoy-domain-of-the-rice-nlr-immune-receptor-rga5
#18
Diana Ortiz, Karine De Guillen, Stella Cesari, Véronique Chalvon, Jérome Gracy, André Padilla, Thomas Kroj
Nucleotide-binding domain and leucine-rich repeat proteins (NLRs) are important receptors in plant immunity that allow recognition of pathogen effectors. The rice NLR RGA5 recognizes the Magnaporthe oryzae effector AVR-Pia through direct interaction. Here, we gained detailed insights into the molecular and structural bases of AVR-Pia-RGA5 interaction and the role of the RATX1 decoy domain of RGA5. NMR titration combined with in vitro and in vivo protein-protein interaction analyses identified the AVR-Pia interaction surface that binds to the RATX1 domain...
January 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28087810/akt1-lkb1-and-yap1-revealed-as-myc-interactors-with-nanoluc-based-protein-fragment-complementation-assay
#19
Xiu-Lei Mo, Qi Qi, Andrei A Ivanov, Qiankun Niu, Yin Luo, Jonathan Havel, Russell Goetze, Sydney Bell, Carlos S Moreno, Lee A D Cooper, Margaret A Johns, Fadlo R Khuri, Yuhong Du, Haian Fu
The c-Myc (MYC) transcription factor is a major cancer driver and a well-validated therapeutic target. However, directly targeting MYC has been challenging. Thus, identifying proteins that interact with and regulate MYC may provide alternative strategies to inhibit its oncogenic activity. Here we report the development of a NanoLuc®-based protein-fragment complementation assay (NanoPCA) and mapping of the MYC protein interaction hub in live mammalian cells. The NanoPCA system was configured to enable detection of protein-protein interactions (PPI) at the endogenous level, as shown with PRAS40 dimerization, and detection of weak interactions, such as PINCH1-NCK2...
January 13, 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/28087739/tnf-signaling-through-rip1-kinase-enhances-sn38-induced-death-in-colon-adenocarcinoma
#20
Lucia Cabal-Hierro, Peter J O'Dwyer
: Elucidation of tumor necrosis factor (TNF)-directed mechanisms for cell death induction and maintenance of tumor growth has revealed a role for receptor-interacting protein kinases 1 and 3 (RIPK1/RIP1 and RIPK3/RIP3), components of the necrosome complex, as determinants of cell fate. Here the participation of TNF signaling was analyzed with regard to the cytotoxic action of different DNA damaging agents in a panel of colon cancer cells. While most of these cell lines were insensitive to TNF, combination with these drugs increased sensitivity by inducing cell death and DNA damage, especially in the case of the topoisomerase inhibitor SN38...
January 13, 2017: Molecular Cancer Research: MCR
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