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Structural Proteomics

Xiaoping Wang, Jianqing Zhao, Cong Cai, Xiaojuan Tang, Lei Fu, Anding Zhang, Li Han
Streptococcus suis ( S. suis ) ranks among the five most important porcine pathogens worldwide and occasionally threatens human health, particularly in people who come into close contact with pigs or pork products. An S. suis infection induces the formation of neutrophil extracellular traps (NETs) in vitro and in vivo , and the NET structure plays an essential role in S. suis clearance. However, the signaling pathway by which S. suis induces NET formation remains to be elucidated. In the present study, we used a label-free quantitative proteomic analysis of mouse NET formation induced by S...
2018: Frontiers in Immunology
Satya Prathyusha Bhamidimarri, Michael Zahn, Jigneshkumar Dahyabhai Prajapati, Christian Schleberger, Sandra Söderholm, Jennifer Hoover, Josh West, Ulrich Kleinekathöfer, Dirk Bumann, Mathias Winterhalter, Bert van den Berg
Research efforts to discover potential new antibiotics for Gram-negative bacteria suffer from high attrition rates due to the synergistic action of efflux systems and the limited permeability of the outer membrane (OM). One strategy to overcome the OM permeability barrier is to identify small molecules that are natural substrates for abundant OM channels and use such compounds as scaffolds for the design of efficiently permeating antibacterials. Here we present a multidisciplinary approach to identify such potential small-molecule scaffolds...
November 15, 2018: Structure
Yu Shen, Jinfeng Li, Ruochen Gu, Xinhua Zhan, Baoshan Xing
The exposure of polycyclic aromatic hydrocarbons (PAHs) can cause wheat leaf chlorosis. Thus, we hypothesize that chloroplast inner structure damage is the reason for leaf chlorosis. This study was conducted with the wheat seedlings exposed to Hoagland nutrient solution containing 1.0 mg L-1 phenanthrene for 9 days. Subcellular observation showed that chloroplast turns round and loses its structural integrity. Herein, iTRAQ (isobaric tag for relative and absolute quantification) was applied to analyze the changes of protein profile in chloroplast exposed to phenanthrene...
December 11, 2018: Environment International
Alaa Kamnaksh, Noora Puhakka, Idrish Ali, Gregory Smith, Roxanne Aniceto, Jesse McCullough, Shalini Das Gupta, Xavier Ekolle Ndode-Ekane, Rhys Brady, Pablo Casillas-Espinosa, Matt Hudson, Cesar Santana-Gomez, Riikka Immonen, Pedro Andrade de Abreu, Nigel Jones, Sandy Shultz, Richard J Staba, Terence J O'Brien, Denes Agoston, Asla Pitkänen
The Epilepsy Bioinformatics Study for Antiepileptogenic Therapy (EpiBioS4Rx) is an international, multicenter, multidisciplinary study aimed at preventing epileptogenesis (EpiBioS4Rx: One of the study's major objectives is the discovery of diagnostic, prognostic, and predictive plasma protein and microRNA (miRNA) biomarkers that are sensitive, specific, and translatable to the human condition. Epilepsy due to structural brain abnormalities, secondary to neurological insults such as traumatic brain injury (TBI), currently represents ∼50% of all epilepsy cases...
November 26, 2018: Epilepsy Research
Karin Jaeger, Supawadee Sukseree, Shaomin Zhong, Brett S Phinney, Veronika Mlitz, Maria Buchberger, Marie Sophie Narzt, Florian Gruber, Erwin Tschachler, Robert H Rice, Leopold Eckhart
Epidermal keratinocytes undergo cornification to form the cellular building blocks of hard skin appendages such as nails and the protective layer on the surface of the skin. Cornification requires the cross-linking of structural proteins and the removal of other cellular components to form mechanically rigid and inert corneocytes. Autophagy has been proposed to contribute to this intracellular remodelling process, but its molecular targets in keratinocytes, if any, have remained elusive. Here, we deleted the essential autophagy factor Atg7 in K14-positive epithelia of mice and determined by proteomics the impact of this deletion on the abundance of individual proteins in cornified nails...
December 14, 2018: Apoptosis: An International Journal on Programmed Cell Death
Friedrich Lottspeich
No abstract text is available yet for this article.
December 2018: EuPA Open Proteomics
Yoori Kim, Christopher M Furman, Carol M Manhart, Eric Alani, Ilya J Finkelstein
Intrinsically disordered regions (IDRs) are present in at least 30% of the eukaryotic proteome and are enriched in chromatin-associated proteins. Using a combination of genetics, biochemistry and single-molecule biophysics, we characterize how IDRs regulate the functions of the yeast MutLα (Mlh1-Pms1) mismatch repair (MMR) complex. Shortening or scrambling the IDRs in both subunits ablates MMR in vivo. Mlh1-Pms1 complexes with shorter IDRs that disrupt MMR retain wild-type DNA binding affinity but are impaired for diffusion on both naked and nucleosome-coated DNA...
December 12, 2018: Nucleic Acids Research
Philippe Colson, Anthony Levasseur, Bernard La Scola, Vikas Sharma, Arshan Nasir, Pierre Pontarotti, Gustavo Caetano-Anollés, Didier Raoult
Giant viruses of amoebae were discovered in 2003. Since then, their diversity has greatly expanded. They were suggested to form a fourth branch of life, collectively named 'TRUC' (for "Things Resisting Uncompleted Classifications") alongside Bacteria , Archaea , and Eukarya . Their origin and ancestrality remain controversial. Here, we specify the evolution and definition of giant viruses. Phylogenetic and phenetic analyses of informational gene repertoires of giant viruses and selected bacteria, archaea and eukaryota were performed, including structural phylogenomics based on protein structural domains grouped into 289 universal fold superfamilies (FSFs)...
2018: Frontiers in Microbiology
Ke Zhang, Guijun Shang, Abhilash Padavannil, Juan Wang, Ramanavelan Sakthivel, Xiang Chen, Min Kim, Matthew G Thompson, Adolfo García-Sastre, Kristen W Lynch, Zhijian J Chen, Yuh Min Chook, Beatriz M A Fontoura
The influenza virulence factor NS1 protein interacts with the cellular NS1-BP protein to promote splicing and nuclear export of the viral M mRNAs. The viral M1 mRNA encodes the M1 matrix protein and is alternatively spliced into the M2 mRNA, which is translated into the M2 ion channel. These proteins have key functions in viral trafficking and budding. To uncover the NS1-BP structural and functional activities in splicing and nuclear export, we performed proteomics analysis of nuclear NS1-BP binding partners and showed its interaction with constituents of the splicing and mRNA export machineries...
December 11, 2018: Proceedings of the National Academy of Sciences of the United States of America
Michal Barski
BACKGROUND: Intrinsic structural disorder is a common property of many proteins, especially in eukaryotic and virus proteomes. The tendency of some proteins or protein regions to exist in a disordered state usually precludes their structural characterisation and renders them especially difficult for experimental handling after recombinant expression. RESULTS: A new intuitive, publicly-available computational resource, called BASILIScan, is presented here. It provides a BLAST-based search for close homologues of the protein of interest, integrated with a simultaneous prediction of intrinsic disorder together with a robust data viewer and interpreter...
December 11, 2018: BMC Genomics
Cunzhi Peng, Lili Chang, Qian Yang, Zheng Tong, Dan Wang, Yanhua Tan, Yong Sun, Xiaoping Yi, Guohua Ding, Junhan Xiao, Ying Zhang, Xuchu Wang
Sesuvium portulacastrum, an important mangrove-associated true halophyte belongs to the family Aizoaceae, has excellent salt tolerance. Chloroplasts are the most sensitive organelles involved in the response to salinity. However, the regulation mechanism of chloroplasts of S. portulacastrum under salinity stress has not been reported. In this study, morphological and physiological analyses of leaves and comparative proteomics of chloroplasts isolated from the leaves of S. portulacastrum under different NaCl treatments were performed...
November 16, 2018: Journal of Plant Physiology
Seul I Kim, Seongok Kim, Eunsuk Kim, Seo Yeon Hwang, Hyunjin Yoon
Outer membrane vesicles (OMVs) are spherical membranous structures released by Gram-negative bacteria. Several bacterial pathogens utilize OMVs as vehicles for the delivery of virulence factors into host cells. Results of our previous study on proteomic analysis revealed that OMVs isolated from Salmonella enterica serovar Typhimurium had virulence effectors that are known to be translocated by Salmonella pathogenicity island 1 (SPI-1)-encoded type III secretion system (T3SS1) into the host cell. In the present study, immunoblot analysis confirmed the secretion of the six T3SS1 effector proteins, namely SipB and SipC (translocators of T3SS1), and SipA, SopA, SopB, and SopE2 (effectors translocated by T3SS1), by OMVs...
2018: Frontiers in Microbiology
David Heckmann, Colton J Lloyd, Nathan Mih, Yuanchi Ha, Daniel C Zielinski, Zachary B Haiman, Abdelmoneim Amer Desouki, Martin J Lercher, Bernhard O Palsson
Knowing the catalytic turnover numbers of enzymes is essential for understanding the growth rate, proteome composition, and physiology of organisms, but experimental data on enzyme turnover numbers is sparse and noisy. Here, we demonstrate that machine learning can successfully predict catalytic turnover numbers in Escherichia coli based on integrated data on enzyme biochemistry, protein structure, and network context. We identify a diverse set of features that are consistently predictive for both in vivo and in vitro enzyme turnover rates, revealing novel protein structural correlates of catalytic turnover...
December 7, 2018: Nature Communications
Imke Baade, Ralph H Kehlenbach
The molecular mechanisms of nuclear transport have been described in great detail and we are beginning to understand the structures of transport complexes and even of subcomplexes of the nuclear pore at an atomic or near-atomic resolution. The complexity of the clients that use the transport machinery, by contrast, is less well understood, although some transport receptors are reported to have hundreds of different cargoes and others only a few. Here, we review the recent attempts to define the cargo spectrum of individual nuclear transport receptors using bioinformatic, biochemical and cell biological approaches and compare the results obtained by these complementary methods...
December 6, 2018: Current Opinion in Cell Biology
Jakob Trendel, Thomas Schwarzl, Rastislav Horos, Ananth Prakash, Alex Bateman, Matthias W Hentze, Jeroen Krijgsveld
Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here, we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs) and to identify hundreds of protein-RNA interfaces...
December 1, 2018: Cell
Sigrid Milles, Nicola Salvi, Martin Blackledge, Malene Ringkjøbing Jensen
Over the last two decades, it has become increasingly clear that a large fraction of the human proteome is intrinsically disordered or contains disordered segments of significant length. These intrinsically disordered proteins (IDPs) play important regulatory roles throughout biology, underlining the importance of understanding their conformational behavior and interaction mechanisms at the molecular level. Here we review recent progress in the NMR characterization of the structure and dynamics of IDPs in various functional states and environments...
December 2018: Progress in Nuclear Magnetic Resonance Spectroscopy
Irina V Novikova, Noopur Sharma, Trevor Moser, Ryan Sontag, Yan Liu, Michael J Collazo, Duilio Cascio, Tolou Shokuhfar, Hanjo Hellmann, Michael Knoblauch, James E Evans
One of the biggest bottlenecks for structural analysis of proteins remains the creation of high-yield and high-purity samples of the target protein. Cell-free protein synthesis technologies are powerful and customizable platforms for obtaining functional proteins of interest in short timeframes, while avoiding potential toxicity issues and permitting high-throughput screening. These methods have benefited many areas of genomic and proteomics research, therapeutics, vaccine development and protein chip constructions...
2018: Advanced Structural and Chemical Imaging
Zhuo Chang, Paolo Paoletti, Maria Lyck Hansen, Hans Christian Beck, Po-Yu Chen, Lars Melholt Rasmussen, Riaz Akhtar
Using the atomic force microscopy- (AFM-) PeakForce quantitative nanomechanical mapping (QNM) technique, we have previously shown that the adventitia of the human internal mammary artery (IMA), tested under dehydrated conditions, is altered in patients with a high degree of arterial stiffening. In this study, we explored the nanoscale elastic modulus of the tunica media of the IMA in hydrated and dehydrated conditions from the patients with low and high arterial stiffening, as assessed in vivo by carotid-femoral pulse wave velocity (PWV)...
2018: Scanning
Xiao-Yan Yang, Jing-Yu Xu, Miao Meng, Nan Li, Chun-Yuan Liu, Qing-Yu He
Drug resistance in bacteria is becoming a significant threat to global public health, and the development of novel and efficient antibacterial compounds is urgently needed. Recently, rhodium complexes have attracted attention as antimicrobial agents, yet their antibacterial mechanism remains unknown. In this study, we observed that the dirhodium (II) complex Rh2 Ac4 inhibited Streptococcus. pneumoniae growth without significant cytotoxic side-effects on host cells in vitro. We subsequently investigated the antibacterial mechanism of Rh2 Ac4 using iTRAQ-based proteomics combined with cellular and biochemical assays...
December 4, 2018: Journal of Proteomics
Anton S Petrov, Elizabeth C Wood, Chad R Bernier, Ashlyn M Norris, Alan Brown, A Amunts
Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data...
December 4, 2018: Molecular Biology and Evolution
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