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Protein function prediction

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https://www.readbyqxmd.com/read/28346509/systematic-identification-of-phosphorylation-mediated-protein-interaction-switches
#1
Matthew J Betts, Oliver Wichmann, Mathias Utz, Timon Andre, Evangelia Petsalaki, Pablo Minguez, Luca Parca, Frederick P Roth, Anne-Claude Gavin, Peer Bork, Robert B Russell
Proteomics techniques can identify thousands of phosphorylation sites in a single experiment, the majority of which are new and lack precise information about function or molecular mechanism. Here we present a fast method to predict potential phosphorylation switches by mapping phosphorylation sites to protein-protein interactions of known structure and analysing the properties of the protein interface. We predict 1024 sites that could potentially enable or disable particular interactions. We tested a selection of these switches and showed that phosphomimetic mutations indeed affect interactions...
March 27, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28346469/computational-identifying-and-characterizing-circular-rnas-and-their-associated-genes-in-hepatocellular-carcinoma
#2
Yan Li, Yongcheng Dong, Ziyan Huang, Qifan Kuang, Yiming Wu, Yizhou Li, Menglong Li
Hepatocellular carcinoma (HCC) is currently still a major factor leading to death, lacking of reliable biomarkers. Therefore, deep understanding the pathogenesis for HCC is of great importance. The emergence of circular RNA (circRNA) provides a new way to study the pathogenesis of human disease. Here, we employed the prediction tool to identify circRNAs based on RNA-seq data. Then, to investigate the biological function of the circRNA, the candidate circRNAs were associated with the protein-coding genes (PCGs) by GREAT...
2017: PloS One
https://www.readbyqxmd.com/read/28346365/an-amylase-like-protein-amyd-is-the-major-negative-regulator-for-%C3%AE-glucan-synthesis-in-aspergillus-nidulans-during-the-asexual-life-cycle
#3
Xiaoxiao He, Shengnan Li, Susan Kaminskyj
α-Glucan affects fungal cell-cell interactions and is important for the virulence of pathogenic fungi. Interfering with production of α-glucan could help to prevent fungal infection. In our previous study, we reported that an amylase-like protein, AmyD, could repress α-glucan accumulation in Aspergillus nidulans. However, the underlying molecular mechanism was not clear. Here, we examined the localization of AmyD and found it was a membrane-associated protein. We studied AmyD function in α-glucan degradation, as well as with other predicted amylase-like proteins and three annotated α-glucanases...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28346356/microinjection-of-antibodies-targeting-the-lamin-a-c-histone-binding-site-blocks-mitotic-entry-and-reveals-separate-chromatin-interactions-with-hp1-cenpb-and-pml
#4
Charles R Dixon, Melpomeni Platani, Alexandr A Makarov, Eric C Schirmer
Lamins form a scaffold lining the nucleus that binds chromatin and contributes to spatial genome organization; however, due to the many other functions of lamins, studies knocking out or altering the lamin polymer cannot clearly distinguish between direct and indirect effects. To overcome this obstacle, we specifically targeted the mapped histone-binding site of A/C lamins by microinjecting antibodies specific to this region predicting that this would make the genome more mobile. No increase in chromatin mobility was observed; however, interestingly, injected cells failed to go through mitosis, while control antibody-injected cells did...
March 25, 2017: Cells
https://www.readbyqxmd.com/read/28345638/lectin-like-oxidized-low-density-lipoprotein-receptor-1-facilitates-metastasis-of-gastric-cancer-through-driving-epithelial-mesenchymal-transition-and-pi3k-akt-gsk3%C3%AE-activation
#5
Can Li, Jie Zhang, Hao Wu, Lili Li, Caiting Yang, Shushu Song, Peike Peng, Miaomiao Shao, Mingming Zhang, Junjie Zhao, Ran Zhao, Weicheng Wu, Yuanyuan Ruan, Lan Wang, Jianxin Gu
Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a pattern recognition receptor that plays a critical role in vascular diseases and host immune response. Recently, our research discovered that LOX-1 could facilitate the uptake of dying cells and cross-presentation of cellular antigen via binding with heat shock proteins, which have a close relationship with gastric neoplasia. Therefore, we speculated that LOX-1 may serve as an oncogene in gastric cancer (GC) development and progression. In this study, through immunohistochemistry staining assay and cancer-related databases, we found that LOX-1 expression was up-regulated in GC tissues and correlated with a poor prognosis in GC patients...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345460/coactivator-associated-arginine-methyltransferase-1-promotes-cell-growth-and-is-targeted-by-microrna-195-5p-in-human-colorectal-cancer
#6
Meifeng Zhang, Wei Wu, Ming Gao, Jie Zhang, Xinde Ding, Ronghua Zhu, Haiqun Chen, Zhewei Fei
The pathogenesis of colorectal cancer remains poorly understood. Here, we show that coactivator-associated arginine methyltransferase 1 is frequently upregulated in colorectal cancer tissues and promotes cell growth in vitro and in vivo. Using bioinformatics-based prediction and luciferase reporter system, we found that coactivator-associated arginine methyltransferase 1 is post-transcriptionally targeted by microRNA-195-5p in colorectal cancer. Ectopic expression of microRNA-195-5p led to the suppression of the coactivator-associated arginine methyltransferase 1 3'-untranslated regions activity and downregulation of the endogenous coactivator-associated arginine methyltransferase 1 protein in colorectal cancer cells...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28344213/over-expression-of-tbl1xr1-indicates-poor-prognosis-of-serous-epithelial-ovarian-cancer
#7
Ming Ma, Nina Yu
Transducin (β)-like 1 X-linked receptor 1 (TBL1XR1) is a core component of the NCoR/SMRT transcription co-repressor complex, and its role in regulating cancer progression has been reported. Serous epithelial ovarian cancer (EOC) is the most common histological type of EOC. Here we explored the significance of TBL1XR1 expression in predicting outcomes of patients with serous EOC. Real-time quantitative PCR analysis showed that the expression level of TBL1XR1 mRNA was significantly higher in EOC tissues compared with adjacent non-tumorous tissues...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28343753/limnothrix-sp-ko05-a-newly-characterized-cyanobacterial-biosorbent-for-cadmium-removal-the-enzymatic-and-non-enzymatic-antioxidant-reactions-to-cadmium-toxicity
#8
Omid Haghighi, Shahab Shahryari, Mojgan Ebadi, Sima Modiri, Hossein Shahbani Zahiri, Hadi Maleki, Kambiz Akbari Noghabi
In this study, we isolated five indigenous cyanobacterial strains from different aqueous environments, with heavy metals contamination, in East Azerbaijan Province (northwest portion of Iran). A strain was identified by morphological and 16S rRNA sequence analysis as Limnothrix sp. KO05 and selected for further studies as having the greatest potential for cadmium uptake. Scanning electron microscopy (SEM) demonstrated cyanobacterium Limnothrix sp. KO05 forms filamentous structures and is straight or curved to some extent...
March 18, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28343629/biallelic-variants-in-otud6b-cause-an-intellectual-disability-syndrome-associated-with-seizures-and-dysmorphic-features
#9
Teresa Santiago-Sim, Lindsay C Burrage, Frédéric Ebstein, Mari J Tokita, Marcus Miller, Weimin Bi, Alicia A Braxton, Jill A Rosenfeld, Maher Shahrour, Andrea Lehmann, Benjamin Cogné, Sébastien Küry, Thomas Besnard, Bertrand Isidor, Stéphane Bézieau, Isabelle Hazart, Honey Nagakura, LaDonna L Immken, Rebecca O Littlejohn, Elizabeth Roeder, Bulent Kara, Katia Hardies, Sarah Weckhuysen, Patrick May, Johannes R Lemke, Orly Elpeleg, Bassam Abu-Libdeh, Kiely N James, Jennifer L Silhavy, Mahmoud Y Issa, Maha S Zaki, Joseph G Gleeson, John R Seavitt, Mary E Dickinson, M Cecilia Ljungberg, Sara Wells, Sara J Johnson, Lydia Teboul, Christine M Eng, Yaping Yang, Peter-Michael Kloetzel, Jason D Heaney, Magdalena A Walkiewicz
Ubiquitination is a posttranslational modification that regulates many cellular processes including protein degradation, intracellular trafficking, cell signaling, and protein-protein interactions. Deubiquitinating enzymes (DUBs), which reverse the process of ubiquitination, are important regulators of the ubiquitin system. OTUD6B encodes a member of the ovarian tumor domain (OTU)-containing subfamily of deubiquitinating enzymes. Herein, we report biallelic pathogenic variants in OTUD6B in 12 individuals from 6 independent families with an intellectual disability syndrome associated with seizures and dysmorphic features...
March 21, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28343125/structural-modeling-of-human-organic-cation-transporters
#10
Tikam Chand Dakal, Rajender Kumar, Dindial Ramotar
Human organic cation transporters (hOCTs) belong to solute carriers (SLC) 22 family of membrane proteins that play a central role in transportation of chemotherapeutic drugs for several clinical and pathological conditions, including cancer and diabetes. These transporters mediate drug transport; however, the precise mechanism of drug-binding and transport by them is not fully uncovered yet, partly due to unavailability of any crystal structure record. In this work, we performed a multi-phasic approach to compute the 3D structural models of seven human organic cation transporters (hOCTs) starting from primary protein sequence...
March 18, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28342242/a-systematic-analysis-of-scoring-functions-in-rigid-body-protein-docking-the-delicate-balance-between-the-predictive-rate-improvement-and-the-risk-of-overtraining
#11
Didier Barradas-Bautista, Iain H Moal, Juan Fernández-Recio
Protein-protein interactions play fundamental roles in biological processes including signaling, metabolism and trafficking. While the structure of a protein complex reveals crucial details about the interaction, it is often difficult to acquire this information experimentally. As the number of interactions discovered increases faster than they can be characterized, protein-protein docking calculations may be able to reduce this disparity by providing models of the interacting proteins. Rigid-body docking is a widely used docking approach, and is often capable of generating a pool of models within which a near-native structure can be found...
March 25, 2017: Proteins
https://www.readbyqxmd.com/read/28341816/increased-expression-of-toll-like-receptors-2-and-4-in-renal-transplant-recipients-that-develop-allograft-dysfunction-a-cohort-study
#12
Morteza Hosseinzadeh, Mohsen Nafar, Pedram Ahmadpoor, Farshid Noorbakhsh, Mir Saeed Yekaninejad, Mohammad Hossein Niknam, Aliakbar Amirzargar
BACKGROUND: The incidence of ischemic reperfusion injury (IRI) in early phase post-transplantation and activation of toll-like receptor (TLR-2) and TLR-4 remarkably impact the outcome of a renal allograft. OBJECTIVE: To investigate whether the expression of TLRs in peripheral blood mononuclear cells (PBMCs) can predict the clinical outcome of kidney allografts. METHODS: We obtained blood samples from 52 renal transplant patients before transplant, and 2, 90, and 180 days post-transplantation in order to analyze the surface expressions of TLR-2 and TLR-4 on peripheral blood monocytes...
March 2017: Iranian Journal of Immunology: IJI
https://www.readbyqxmd.com/read/28341448/the-drosophila-dock-family-protein-sponge-is-required-for-development-of-the-air-sac-primordium
#13
Kazushge Morishita, Dang Ngoc Anh Suong, Hideki Yoshida, Masamitsu Yamaguchi
Dedicator of cytokinesis (DOCK) family genes are known as DOCK1-DOCK11 in mammals. DOCK family proteins mainly regulate actin filament polymerization and/or depolymerization and are GEF proteins, which contribute to cellular signaling events by activating small G proteins. Sponge (Spg) is a Drosophila counterpart to mammalian DOCK3/DOCK4, and plays a role in embryonic central nervous system development, R7 photoreceptor cell differentiation, and adult thorax development. In order to conduct further functional analyses on Spg in vivo, we examined its localization in third instar larval wing imaginal discs...
March 21, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28341438/engineering-a-novel-porin-ompgf-via-strand-replacement-from-computational-analysis-of-sequence-motif
#14
Meishan Lin, Ge Zhang, Monifa Fahie, Leslie K Morgan, Min Chen, Timothy A Keiderling, Linda J Kenney, Jie Liang
β -barrel membrane proteins (βMPs) form barrel-shaped pores in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Because of the robustness of their barrel structures, βMPs have great potential as nanosensors for single-molecule detection. However, natural βMPs currently employed have inflexible biophysical properties and are limited in their pore geometry, hindering their applications in sensing molecules of different sizes and properties. Computational engineering has the promise to generate βMPs with desired properties...
March 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28340571/dirprot-a-computational-approach-for-discriminating-insecticide-resistant-proteins-from-non-resistant-proteins
#15
Prabina Kumar Meher, Tanmaya Kumar Sahu, Anjali Banchariya, Atmakuri Ramakrishna Rao
BACKGROUND: Insecticide resistance is a major challenge for the control program of insect pests in the fields of crop protection, human and animal health etc. Resistance to different insecticides is conferred by the proteins encoded from certain class of genes of the insects. To distinguish the insecticide resistant proteins from non-resistant proteins, no computational tool is available till date. Thus, development of such a computational tool will be helpful in predicting the insecticide resistant proteins, which can be targeted for developing appropriate insecticides...
March 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28340510/the-diverse-family-of-mmpl-transporters-in-mycobacteria-from-regulation-to-antimicrobial-developments
#16
REVIEW
Albertus Viljoen, Violaine Dubois, Fabienne Girard-Misguich, Mickael Blaise, Jean-Louis Herrmann, Laurent Kremer
Mycobacterial genomes contain large sets of loci encoding membrane proteins that belong to a family of multidrug resistance pumps designated Resistance-Nodulation-Cell Division (RND) permeases. Mycobacterial membrane protein Large (MmpL) transporters represent a subclass of RND transporters known to participate in the export of lipid components across the cell envelope. These surface-exposed lipids with unusual structures play key roles in the physiology of mycobacteria and/or can act as virulence factors and immunomodulators...
March 24, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28340487/microrna-4739-regulates-osteogenic-and-adipocytic-differentiation-of-immortalized-human-bone-marrow-stromal-cells-via-targeting-lrp3
#17
Mona Elsafadi, Muthurangan Manikandan, Nehad M Alajez, Rimi Hamam, Raed Abu Dawud, Abdullah Aldahmash, Zafar Iqbal, Musaad Alfayez, Moustapha Kassem, Amer Mahmood
Understanding the regulatory networks underlying lineage differentiation and fate determination of human bone marrow stromal cells (hBMSC) is a prerequisite for their therapeutic use. The goal of the current study was to unravel the novel role of the low-density lipoprotein receptor-related protein 3 (LRP3) in regulating the osteogenic and adipogenic differentiation of immortalized hBMSCs. Gene expression profiling revealed significantly higher LRP3 levels in the highly osteogenic hBMSC clone imCL1 than in the less osteogenic clone imCL2, as well as a significant upregulation of LRP3 during the osteogenic induction of the imCL1 clone...
March 8, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28339599/a-single-nucleotide-polymorphism-in-coq9-affects-mitochondrial-and-ovarian-function-and-fertility-in-holstein-cows%C3%A2
#18
M Sofia Ortega, Stephanie Wohlgemuth, Paula Tribulo, Luiz G B Siqueira, Daniel J Null, John B Cole, Marcus V Da Silva, Peter J Hansen
A single missense mutation at position 159 of coenzyme Q9 (COQ9) (G→A; rs109301586) has been associated with genetic variation in fertility in Holstein cattle, with the A allele associated with higher fertility. COQ9 is involved in the synthesis of coenzyme COQ10, a component of the electron transport system of the mitochondria. Here we tested whether reproductive phenotype is associated with the mutation and evaluated functional consequences for cellular oxygen metabolism, body weight changes, and ovarian function...
February 3, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28339482/a-genome-wide-identification-and-analysis-of-the-dyw-deaminase-genes-in-the-pentatricopeptide-repeat-gene-family-in-cotton-gossypium-spp
#19
Bingbing Zhang, Guoyuan Liu, Xue Li, Liping Guo, Xuexian Zhang, Tingxiang Qi, Hailin Wang, Huini Tang, Xiuqin Qiao, Jinfa Zhang, Chaozhu Xing, Jianyong Wu
The RNA editing occurring in plant organellar genomes mainly involves the change of cytidine to uridine. This process involves a deamination reaction, with cytidine deaminase as the catalyst. Pentatricopeptide repeat (PPR) proteins with a C-terminal DYW domain are reportedly associated with cytidine deamination, similar to members of the deaminase superfamily. PPR genes are involved in many cellular functions and biological processes including fertility restoration to cytoplasmic male sterility (CMS) in plants...
2017: PloS One
https://www.readbyqxmd.com/read/28339066/microrna%C3%A2-499-rs3746444-a-g-polymorphism-functions-as-a-biomarker-to-predict-recurrence-following-endoscopic-submucosal-dissection-in-primary-early-gastric-cancer
#20
Huiyong Shi, Xiangshan Yang, Yanan Zhen, Shoujun Huo, Ruixue Xiao, Zhongfa Xu
The aim of the present study was to investigate the molecular mechanism, including the potential regulatory and signaling pathways, of platelet‑derived growth factor receptor β (PDGFRB), which underlies the recurrence of early gastric cancer (EGC) following endoscopic submucosal dissection (ESD). Online microRNA (miRNA) target prediction tools were used, which identified PDGFRB as the candidate target gene of miR‑499a in gastric cancer cells, and PFGRBR was then confirmed as the direct gene using a luciferase reporter assay system...
March 23, 2017: Molecular Medicine Reports
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