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Structural Proteomics

Silvia Buroni, Viola C Scoffone, Marco Fumagalli, Vadim Makarov, Maddalena Cagnone, Gabriele Trespidi, Edda De Rossi, Federico Forneris, Giovanna Riccardi, Laurent R Chiarelli
Quorum sensing (QS) is a bacterial intercellular communication process which controls the production of major virulence factors, such as proteases, siderophores, and toxins, as well as biofilm formation. Since the inhibition of this pathway reduces bacterial virulence, QS is considered a valuable candidate drug target, particularly for the treatment of opportunistic infections, such as those caused by Burkholderia cenocepacia in cystic fibrosis patients. Diketopiperazine inhibitors of the acyl homoserine lactone synthase CepI have been recently described...
2018: Frontiers in Pharmacology
Sirish K Ippagunta, Julie A Pollock, Naina Sharma, Wenwei Lin, Taosheng Chen, Kazuki Tawaratsumida, Anthony A High, Jaeki Min, Yizhe Chen, R Kiplin Guy, Vanessa Redecke, John A Katzenellenbogen, Hans Häcker
Toll-like receptors (TLRs) recognize various pathogen- and host tissue-derived molecules and initiate inflammatory immune responses. Exaggerated or prolonged TLR activation, however, can lead to etiologically diverse diseases, such as bacterial sepsis, metabolic and autoimmune diseases, or stroke. Despite the apparent medical need, no small-molecule drugs against TLR pathways are clinically available. This may be because of the complex signaling mechanisms of TLRs, which are governed by a series of protein-protein interactions initiated by Toll/interleukin-1 receptor homology domains (TIR) found in TLRs and the cytoplasmic adaptor proteins TIRAP and MyD88...
August 14, 2018: Science Signaling
Anu Manhas, Anjali Patel, Mohsin Y Lone, Prafulla K Jha, Prakash C Jha
In the current study, we have constructed receptor-based pharmacophore models by exploiting the Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR) structural proteome. The derived models were subjected to a series of validation procedures to list the representative hypotheses that can be used for the screening of the Drug-like Diverse Database. A set of 739 molecules was retrieved and analyzed for the adsorption, distribution, metabolism, excretion and toxicity (ADMET) and drug-likeness attributes...
August 13, 2018: Journal of Cellular Biochemistry
Keriann M Backus
Cysteine thiols are involved in a diverse set of biological transformations, including nucleophilic and redox catalysis, metal coordination and formation of both dynamic and structural disulfides. Often posttranslationally modified, cysteines are also frequently alkylated by electrophilic compounds, including electrophilic metabolites, drugs, and natural products, and are attractive sites for covalent probe and drug development. Quantitative proteomics combined with activity-based protein profiling has been applied to annotate cysteine reactivity, susceptibility to posttranslational modifications, and accessibility to chemical probes, uncovering thousands of functional and small-molecule targetable cysteines across a diverse set of proteins, proteome-wide in an unbiased manner...
August 14, 2018: Current Topics in Microbiology and Immunology
Camille I Pataki, João Rodrigues, Lichao Zhang, Junyang Qian, Bradley Efron, Trevor Hastie, Joshua E Elias, Michael Levitt, Ron R Kopito
Despite not spanning phospholipid bilayers, monotopic integral proteins (MIPs) play critical roles in organizing biochemical reactions on membrane surfaces. Defining the structural basis by which these proteins are anchored to membranes has been hampered by the paucity of unambiguously identified MIPs and a lack of computational tools that accurately distinguish monolayer-integrating motifs from bilayer-spanning transmembrane domains (TMDs). We used quantitative proteomics and statistical modeling to identify 87 high-confidence candidate MIPs in lipid droplets, including 21 proteins with predicted TMDs that cannot be accommodated in these monolayer-enveloped organelles...
August 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
Yang Wu, Simon C Wagstaff, Saeed A Al-Harthi, Alister G Craig
BACKGROUND: To understand more about changes to the molecular components that occur when host endothelium interacts with Plasmodium falciparum-infected erythrocytes, a combined technique of protein separation (1D Blue-Native electrophoresis) and mass spectrometry of infected erythrocytes with endothelial cells (EC) in a co-culture system has been used. METHODS: Native proteins were extracted from co-cultures and identified by mass spectrometry. Proteomic data from different parasite strains, either adhesion proficient (to endothelial cells) or non-adherent, were analysed in parallel to reveal protein associations linked to cytoadherence...
August 13, 2018: Malaria Journal
Trang H Phan, Lisanne M van Leeuwen, Coen Kuijl, Roy Ummels, Gunny van Stempvoort, Alba Rubio-Canalejas, Sander R Piersma, Connie R Jiménez, Astrid M van der Sar, Edith N G Houben, Wilbert Bitter
The pathogen Mycobacterium tuberculosis employs a range of ESX-1 substrates to manipulate the host and build a successful infection. Although the importance of ESX-1 secretion in virulence is well established, the characterization of its individual components and the role of individual substrates is far from complete. Here, we describe the functional characterization of the Mycobacterium marinum accessory ESX-1 proteins EccA1, EspG1 and EspH, i.e. proteins that are neither substrates nor structural components...
August 13, 2018: PLoS Pathogens
Chen Wang, Lukasz Kurgan
Drug-protein interactions (DPIs) underlie the desired therapeutic actions and the adverse side effects of a significant majority of drugs. Computational prediction of DPIs facilitates research in drug discovery, characterization and repurposing. Similarity-based methods that do not require knowledge of protein structures are particularly suitable for druggable genome-wide predictions of DPIs. We review 35 high-impact similarity-based predictors that were published in the past decade. We group them based on three types of similarities and their combinations that they use...
August 8, 2018: Briefings in Bioinformatics
Claudio Schmidli, Luca Rima, Stefan A Arnold, Thomas Stohler, Anastasia Syntychaki, Andrej Bieri, Stefan Albiez, Kenneth N Goldie, Mohamed Chami, Henning Stahlberg, Thomas Braun
Due to recent technological progress, cryo-electron microscopy (cryo-EM) is rapidly becoming a standard method for the structural analysis of protein complexes to atomic resolution. However, protein isolation techniques and sample preparation methods for EM remain a bottleneck. A relatively small number (100,000 to a few million) of individual protein particles need to be imaged for the high-resolution analysis of proteins by the single particle EM approach, making miniaturized sample handling techniques and microfluidic principles feasible...
July 27, 2018: Journal of Visualized Experiments: JoVE
Sven Hennig, Saskia Neubacher
Cellular functions of RNA are no longer limited to their role as blueprints for protein synthesis. Especially noncoding RNA, such as, snRNAs, lncRNAs, miRNAs, play important roles. With increasing numbers of RNAs being identified, it is well known that the transcriptome outnumbers the proteome by far. This emphasizes the great importance of functional RNA characterization and the need to further develop the toolbox for these investigations, of which many are still in their infancy. Fluorescent Light-up APtamers (FLAPs) are RNA sequences that can bind nontoxic, cell-permeable, small-molecule fluorogens and enhance their fluorescence over many orders of magnitude upon binding...
August 13, 2018: Angewandte Chemie
Suli Zhang, Mingming Wei, Mingming Yue, Pengli Wang, Xiaochen Yin, Li Wang, Xiaoli Yang, Huirong Liu
OBJECTIVE: Insulin resistance is highly associated with an adverse intrauterine environment. We previously reported that fetal rats exposed to angiotensin II type 1 receptor (AT1 R) autoantibody (AT1-AA) displayed increased susceptibility to metabolic diseases during middle age. However, the timing of the onset of insulin resistance remains unknown. In this study, we examined the offspring of AT1-AA-positive rats, tracking the development of insulin resistance. METHODS: Pregnant rats were intravenously injected with AT1-AA...
August 12, 2018: Endocrine
Frédéric Deschoenmaeker, Shoko Mihara, Tatsuya Niwa, Hideki Taguchi, Ken-Ichi Wakabayashi, Toru Hisabori
Thioredoxin (Trx) family proteins perform redox regulation in cells, and they are involved in several other biological processes (e.g., oxidative stress tolerance). In the filamentous cyanobacterium Anabaena sp. PCC7120 (A. 7120), eight Trx isoforms have been identified via genomic analysis. Among these Trx isoforms, the absence of Trx-m1 and TrxC appear to result in oxidative stress in A. 7120 together with alterations of the thylakoid membrane structure and phycobiliprotein composition. To thoroughly analyze the physiological changes in these Trx disruptants, quantitative proteomics was applied...
August 8, 2018: Plant & Cell Physiology
Fanchi Meng, Lukasz Kurgan
Intrinsically disordered regions lack stable structure in their native conformation but are nevertheless functional and highly abundant, particularly in Eukaryotes. Disordered moonlighting regions (DMRs) are intrinsically disordered regions that carry out multiple functions. DMRs are different from moonlighting proteins that could be structured and that are annotated at the whole-protein level. DMRs cannot be identified by current predictors of functions of disorder that focus on specific functions rather than multifunctional regions...
August 11, 2018: Proteins
Hans A V Kistemaker, Jim Voorneveld, Dmitri V Filippov
Synthetic mono-ADPr-peptides are useful for structural, biochemical, and proteomics studies. We describe here a protocol for the preparation of mono-ADPr-peptides based on a fairly standard Fmoc-based solid-phase synthesis. Phosphoribosylated precursor building blocks are introduced into the peptide chain on solid-phase and subsequently converted to ADPr-sites by chemical phosphorylation with adenosine phosphoramidite. Suitably protected phosphoribosylated glutamine, asparagine, and citrulline building blocks described in this protocol allow introduction of ADP-Gln, ADPr-Asn, and ADPr-Cit into peptide chains as demonstrated for three peptides...
2018: Methods in Molecular Biology
Weijian Cen, Jianbin Liu, Siyuan Lu, Peilong Jia, Kai Yu, Yue Han, Rongbai Li, Jijing Luo
BACKGROUND: Rice (Oryza sativa L.) is a thermophilic crop vulnerable to chilling stress. However, common wild rice (Oryza rufipogon Griff.) in Guangxi (China) has the ability to tolerate chilling stress. To better understand the molecular mechanisms underlying chilling tolerance in wild rice, iTRAQ-based proteomic analysis was performed to examine CTS-12, a major chilling tolerance QTL derived from common wild rice, mediated chilling and recovery-induced differentially expressed proteins (DEPs) between the chilling-tolerant rice line DC90 and the chilling-sensitive 9311...
August 10, 2018: BMC Plant Biology
Florian Gautier, Kateřina Eliášová, Jean-Charles Leplé, Zuzana Vondráková, Anne-Marie Lomenech, Claire Le Metté, Philippe Label, Guy Costa, Jean-François Trontin, Caroline Teyssier, Marie-Anne Lelu-Walter
BACKGROUND: To explore poorly understood differences between primary and subsequent somatic embryogenic lines of plants, we induced secondary (2ry ) and tertiary (3ry ) lines from cotyledonary somatic embryos (SEs) of two Douglas-fir genotypes: SD4 and TD17. The 2ry lines exhibited significantly higher embryogenic potential (SE yields) than the 1ry lines initiated from zygotic embryos (SD4, 2155 vs 477; TD17, 240 vs 29 g- 1 f.w.). Moreover, we observed similar differences in yield between 2ry and 3ry lines of SD4 (2400 vs 3921 g- 1 f...
August 10, 2018: BMC Plant Biology
Mohanalakshmi Narasumani, Paul M Harrison
Intrinsically disordered regions (IDRs) of proteins play significant biological functional roles despite lacking a well-defined 3D structure. For example, IDRs provide efficient housing for large numbers of post-translational modification (PTM) sites in eukaryotic proteins. Here, we study the distribution of more than 15,000 experimentally determined human methylation, acetylation and ubiquitination sites (collectively termed 'MAU' sites) in ordered and disordered regions, and analyse their conservation across 380 eukaryotic species...
August 10, 2018: PLoS Computational Biology
Harunori Yoshikawa, Mark Larance, Dylan J Harney, Ramasubramanian Sundaramoorthy, Tony Ly, Tom Owen-Hughes, Angus I Lamond
We describe Ribo Mega-SEC, a powerful approach for the separation and biochemical analysis of mammalian polysomes and ribosomal subunits using Size Exclusion Chromatography and uHPLC. Using extracts from either cells, or tissues, polysomes can be separated within 15 min from sample injection to fraction collection. Ribo Mega-SEC shows translating ribosomes exist predominantly in polysome complexes in human cell lines and mouse liver tissue. Changes in polysomes are easily quantified between treatments, such as the cellular response to amino acid starvation...
August 10, 2018: ELife
Sunny Sharma, Johannes David Hartmann, Peter Watzinger, Arvid Klepper, Christian Peifer, Peter Kötter, Denis L J Lafontaine, Karl-Dieter Entian
The entire chemical modification repertoire of yeast ribosomal RNAs and the enzymes responsible for it have recently been identified. Nonetheless, in most cases the precise roles played by these chemical modifications in ribosome structure, function and regulation remain totally unclear. Previously, we demonstrated that yeast Rrp8 methylates m1 A645 of 25S rRNA in yeast. Here, using mung bean nuclease protection assays in combination with quantitative RP-HPLC and primer extension, we report that 25S/28S rRNA of S...
August 9, 2018: Scientific Reports
Cassandra M Modahl, Seth E Frietze, Stephen P Mackessy
High-throughput technologies were used to identify venom gland toxin expression and to characterize the venom proteomes of two rear-fanged snakes, Ahaetulla prasina (Asian Green Vine Snake) and Borikenophis portoricensis (Puerto Rican Racer). Sixty-nine complete toxin-coding transcripts from 12 venom protein superfamilies (A. prasina) and 50 complete coding transcripts from 11 venom protein superfamilies (B. portoricensis) were identified in the venom glands. However, only 18% (A. prasina) and 32% (B. portoricensis) of the translated protein isoforms were detected in the proteome of these venoms...
August 6, 2018: Journal of Proteomics
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