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Ratana Thanasomboon, Saowalak Kalapanulak, Supatcharee Netrphan, Treenut Saithong
Cassava is a starchy root crop whose role in food security becomes more significant nowadays. Together with the industrial uses for versatile purposes, demand for cassava starch is continuously growing. However, in-depth study to uncover the mystery of cellular regulation, especially the interaction between proteins, is lacking. To reduce the knowledge gap in protein-protein interaction (PPI), genome-scale PPI network of cassava was constructed using interolog-based method (MePPI-In, available at http://bml...
December 8, 2017: Scientific Reports
Fan Liu, Philip Lössl, Beverley M Rabbitts, Robert S Balaban, Albert J R Heck
Mitochondria exert an immense amount of cytophysiological functions, but the structural basis of most of these processes is still poorly understood. Here we use cross-linking mass spectrometry to probe the organization of proteins in native mouse heart mitochondria. Our approach provides the largest survey of mitochondrial protein interactions reported so far. In total, we identify 3,322 unique residue-to-residue contacts involving half of the mitochondrial proteome detected by bottom-up proteomics. The obtained mitochondrial protein interactome gives insights in the architecture of defined protein assemblies, the sub-mitochondrial localization, and the mitochondrial localization of five proteins not yet included in the MitoCarta database...
December 8, 2017: Molecular & Cellular Proteomics: MCP
Sarvenaz Sarabipour, Feilim Mac Gabhann
No abstract text is available yet for this article.
December 8, 2017: Biochemistry
Monica Agrawal, Marinka Zitnik, Jure Leskovec
Discovering disease pathways, which can be defined as sets of proteins associated with a given disease, is an important problem that has the potential to provide clinically actionable insights for disease diagnosis, prognosis, and treatment. Computational methods aid the discovery by relying on protein-protein interaction (PPI) networks. They start with a few known disease-associated proteins and aim to find the rest of the pathway by exploring the PPI network around the known disease proteins. However, the success of such methods has been limited, and failure cases have not been well understood...
2018: Pacific Symposium on Biocomputing
Ran Wei, Tomonori Kaneko, Xuguang Liu, Huadong Liu, Lei Li, Courtney Voss, Eric Liu, Ningning He, Shawn S C Li
Cellular functions are frequently regulated by protein-protein interactions involving the binding of a modular domain in one protein to a specific peptide sequence in another.  This mechanism may be explored to identify binding partners for proteins harboring a peptide-recognition domain. Here we report a proteomic strategy combining peptide and protein microarray screening with biochemical and cellular assays to identify modular domain-mediated protein-protein interactions in a systematic manner. We applied this strategy to Numb, a multi-functional protein containing a phosphotyrosine-binding (PTB) domain...
December 7, 2017: Molecular & Cellular Proteomics: MCP
Samantha Moore, Aino I Järvelin, Ilan Davis, Gareth L Bond, Alfredo Castello
Cancer development involves the stepwise accumulation of genetic lesions that overcome the normal regulatory pathways that prevent unconstrained cell division and tissue growth. Identification of the genetic changes that cause cancer has long been the subject of intensive study, leading to the identification of several RNA-binding proteins (RBPs) linked to cancer. Cross-reference of the complement of RBPs recently identified by RNA interactome capture with cancer-associated genes and biological processes led to the identification of a set of 411 proteins with potential implications in cancer biology...
December 4, 2017: Current Opinion in Genetics & Development
Arthur Fischbach, Annika Krüger, Stephanie Hampp, Greta Assmann, Lisa Rank, Matthias Hufnagel, Martin T Stöckl, Jan M F Fischer, Sebastian Veith, Pascal Rossatti, Magdalena Ganz, Elisa Ferrando-May, Andrea Hartwig, Karin Hauser, Lisa Wiesmüller, Alexander Bürkle, Aswin Mangerich
The post-translational modification poly(ADP-ribosyl)ation (PARylation) plays key roles in genome maintenance and transcription. Both non-covalent poly(ADP-ribose) binding and covalent PARylation control protein functions, however, it is unknown how the two modes of modification crosstalk mechanistically. Employing the tumor suppressor p53 as a model substrate, this study provides detailed insights into the interplay between non-covalent and covalent PARylation and unravels its functional significance in the regulation of p53...
December 4, 2017: Nucleic Acids Research
Sahar Melamed, Raya Faigenbaum-Romm, Asaf Peer, Niv Reiss, Omer Shechter, Amir Bar, Yael Altuvia, Liron Argaman, Hanah Margalit
Small RNAs (sRNAs) are major post-transcriptional regulators of gene expression in bacteria. To enable transcriptome-wide mapping of bacterial sRNA-target pairs, we developed RIL-seq (RNA interaction by ligation and sequencing). RIL-seq is an experimental-computational methodology for capturing sRNA-target interactions in vivo that takes advantage of the mutual binding of the sRNA and target RNA molecules to the RNA chaperone protein Hfq. The experimental part of the protocol involves co-immunoprecipitation of Hfq and bound RNAs, ligation of RNAs, library preparation and sequencing...
January 2018: Nature Protocols
Rashid Manzoor, Manabu Igarashi, Ayato Takada
Influenza A virus (IAV) matrix protein 2 (M2) is among the smallest bona fide, hence extensively studied, ion channel proteins. The M2 ion channel activity is not only essential for virus replication, but also involved in modulation of cellular homeostasis in a variety of ways. It is also the target for ion channel inhibitors, i.e., anti-influenza drugs. Thus far, several studies have been conducted to elucidate its biophysical characteristics, structure-function relationships of the ion channel, and the M2-host interactome...
December 7, 2017: International Journal of Molecular Sciences
Andrea Molinas, Maria V Turkina, Karl-Eric Magnusson, Ali Mirazimi, Elena Vikström
Normal epithelial and endothelial renewal and healing after bacterial and viral challenges are essential for homeostasis along the intestine and the blood and lymphatic vessels. We thus investigated whether and how virus affects migration of human epithelial cells and specifically how the nucleocapsid protein (N) modulates the cellular proteome and interactome using human Caco-2 cells in a wound-healing assay with Hazara virus as a model. Here, Hazara virus blocked cell migration in a dose- and time-dependent manner, disrupted the actin cytoskeleton and specifically reduced the expression of the IQ-motif-containing GTPase-activating protein 1 (IQGAP1) and water channel aquaporin 6 (AQP6) that regulate cytoskeletal organization, water homeostasis and vesicle communication...
2017: Frontiers in Cell and Developmental Biology
Rachel A Knoener, Jordan T Becker, Mark Scalf, Nathan M Sherer, Lloyd M Smith
HIV-1 replication requires myriad interactions between cellular proteins and the viral unspliced RNA. These interactions are important in archetypal RNA processes such as transcription and translation as well as for more specialized functions including alternative splicing and packaging of unspliced genomic RNA into virions. We present here a hybridization capture strategy for purification of unspliced full-length HIV RNA-protein complexes preserved in vivo by formaldehyde crosslinking, and coupled with mass spectrometry to identify HIV RNA-protein interactors in HIV-1 infected cells...
December 5, 2017: Scientific Reports
John J Skinner, Sheng Wang, Jiyoung Lee, Colin Ong, Ruth Sommese, Sivaraj Sivaramakrishnan, Wolfgang Koelmel, Maria Hirschbeck, Hermann Schindelin, Caroline Kisker, Kristina Lorenz, Tobin R Sosnick, Marsha Rich Rosner
Phosphorylation is a major regulator of protein interactions; however, the mechanisms by which regulation occurs are not well understood. Here we identify a salt-bridge competition or "theft" mechanism that enables a phospho-triggered swap of protein partners by Raf Kinase Inhibitory Protein (RKIP). RKIP transitions from inhibiting Raf-1 to inhibiting G-protein-coupled receptor kinase 2 upon phosphorylation, thereby bridging MAP kinase and G-Protein-Coupled Receptor signaling. NMR and crystallography indicate that a phosphoserine, but not a phosphomimetic, competes for a lysine from a preexisting salt bridge, initiating a partial unfolding event and promoting new protein interactions...
December 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
Elise Biquand, Juline Poirson, Marwah Karim, Marion Declercq, Nicolas Malausse, Patricia Cassonnet, Cyril Barbezange, Marie-Laure Straub, Louis Jones, Sandie Munier, Nadia Naffakh, Sylvie van der Werf, Yves Jacob, Murielle Masson, Caroline Demeret
The optimized exploitation of cell resources is one cornerstone of a successful infection. Differential mapping of host-pathogen protein-protein interactions (PPIs) on the basis of comparative interactomics of multiple strains is an effective strategy to highlight correlations between host proteome hijacking and biological or pathogenic traits. Here, we developed an interactomic pipeline to deliver high-confidence comparative maps of PPIs between a given pathogen and the human ubiquitin proteasome system (UPS)...
November 2017: MSphere
Mostafa Rezaei Tavirani, Farshad OkHOVATIAN, Mona Zamanian Azodi, Majid Rezaei Tavirani
Objective: Duchenne muscular dystrophy (DMD) is one of the mortal diseases, subjected to study in terms of molecular investigation. In this study, the protein interaction map of this muscle-wasting condition was generated to gain a better knowledge of interactome profile of DMD. Materials & Methods: Applying Cytoscape and String Database, the protein-protein interaction network was constructed and the gene ontology of the constructed network was analyzed for biological process, molecular function, and cellular component annotations...
2017: Iranian Journal of Child Neurology
Paulami Chatterjee, Debjani Roy, Nitin Rathi
BACKGROUND: Epigenetics has emerged as an important field in drug discovery. Alzheimer's disease (AD), the leading neurodegenerative disorder throughout the world, is shown to have an epigenetic basis. Currently, there are very few effective epigenetic drugs available for AD. OBJECTIVE: In this work, for the first time we have proposed 14 AD repositioning epigenetic drugs and identified their targets from extensive human interactome. METHODS: Interacting partners of the AD epigenetic proteins were identified from the extensive human interactome to construct Epigenetic Protein-Protein Interaction Network (EP-PPIN)...
2018: Journal of Alzheimer's Disease: JAD
Sanathoi Gurumayum, Rahul Brahma, Leimarembi Devi Naorem, Mathavan Muthaiyan, Jeyakodi Gopal, Amouda Venkatesan
Re-emergence of ZIKV has caused infections in more than 1.5 million people. The molecular mechanism and pathogenesis of ZIKV is not well explored due to unavailability of adequate model and lack of publically accessible resources to provide information of ZIKV-Human protein interactome map till today. This study made an attempt to curate the ZIKV-Human interaction proteins from published literatures and RNA-Seq data. 11 direct interaction, 12 associated genes are retrieved from literatures and 3742 Differentially Expressed Genes (DEGs) are obtained from RNA-Seq analysis...
November 30, 2017: Virology
Nouha Bouayed Abdelmoula, Balkiss Abdelmoula, Walid Smaoui, Imen Trabelsi, Rim Louati, Samir Aloulou, Wafa Aloulou, Fatma Abid, Senda Kammoun, Khaled Trigui, Olfa Bedoui, Hichem Denguir, Souad Mallek, Mustapha Ben Aziza, Jamila Dammak, Oldez Kaabi, Nawel Abdellaoui, Fatma Turki, Asma Kaabi, Wafa Kamoun, Jihen Jabeur, Wided Ltaif, Kays Chaker, Haytham Fourati, Samir M'rabet, Hedi Ben Ameur, Naourez Gouia, Mohamed Nabil Mhiri, Tarek Rebai
In the era of the diseasomes and interactome networks, linking genetics with phenotypic traits in Turner syndrome should be studied thoroughly. As a part of this stratagem, mosaicism of both X and Y chromosome which is a common finding in TS and an evaluation of congenital heart diseases in the different situations of mosaic TS types, can be helpful in the identification of disturbed sex chromosomes, genes and signaling pathway actors. Here we report the case of a mosaic TS associated to four left-sided CHD, including BAV, COA, aortic aneurysms and dissections at an early age...
December 1, 2017: Molecular Genetics and Genomics: MGG
Shao-Min Wu, Hsuan Liu, Po-Jung Huang, Ian Yi-Feng Chang, Chi-Ching Lee, Chia-Yu Yang, Wen-Sy Tsai, Bertrand Chin-Ming Tan
Background: Despite their lack of protein-coding potential, lncRNAs and circRNAs have emerged as key determinants in gene regulation, acting to fine-tune transcriptional and signaling output. These non-coding RNA transcripts are known to affect expression of messenger RNAs (mRNAs) via epigenetic and post-transcriptional regulation. Given their widespread target spectrum as well as extensive modes of action, a complete understanding of their biological relevance will depend on integrative analyses of systems data at various levels...
November 29, 2017: GigaScience
Michael Solarski, Hansen Wang, Holger Wille, Gerold Schmitt-Ulms
The amyloid beta (Aβ) peptide is central to the pathogenesis of Alzheimer's disease (AD). Insights into Aβ-interacting proteins are critical for understanding the molecular mechanisms underlying Aβ-mediated toxicity. We recently undertook an in-depth in vitro interrogation of the Aβ1-42 interactome using human frontal lobes as the biological source material and taking advantage of advances in mass spectrometry performance characteristics. These analyses uncovered the small cyclic neuropeptide somatostatin (SST) to be the most selectively enriched binder to oligomeric Aβ1-42...
December 1, 2017: Prion
Lesley-Ann Martin, Ricardo Ribas, Nikiana Simigdala, Eugene Schuster, Sunil Pancholi, Tencho Tenev, Pascal Gellert, Laki Buluwela, Alison Harrod, Allan Thornhill, Joanna Nikitorowicz-Buniak, Amandeep Bhamra, Marc-Olivier Turgeon, George Poulogiannis, Qiong Gao, Vera Martins, Margaret Hills, Isaac Garcia-Murillas, Charlotte Fribbens, Neill Patani, Zheqi Li, Matthew J Sikora, Nicholas Turner, Wilbert Zwart, Steffi Oesterreich, Jason Carroll, Simak Ali, Mitch Dowsett
Resistance to endocrine therapy remains a major clinical problem in breast cancer. Genetic studies highlight the potential role of estrogen receptor-α (ESR1) mutations, which show increased prevalence in the metastatic, endocrine-resistant setting. No naturally occurring ESR1 mutations have been reported in in vitro models of BC either before or after the acquisition of endocrine resistance making functional consequences difficult to study. We report the first discovery of naturally occurring ESR1 Y537C and ESR1 Y537S mutations in MCF7 and SUM44 ESR1-positive cell lines after acquisition of resistance to long-term-estrogen-deprivation (LTED) and subsequent resistance to fulvestrant (ICIR)...
November 30, 2017: Nature Communications
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