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Protein structure prediction

Gesine Behrens, Reinhard Winzen, Nina Rehage, Anneke Dörrie, Monika Barsch, Anne Hoffmann, Jörg Hackermüller, Christopher Tiedje, Vigo Heissmeyer, Helmut Holtmann
The expression of proteins during inflammatory and immune reactions is coordinated by post-transcriptional mechanisms. A particularly strong suppression of protein expression is exerted by a conserved translational silencing element (TSE) identified in the 3' UTR of NFKBIZ mRNA, which is among the targets of the RNA-binding proteins Roquin-1/2 and MCPIP1/Regnase-1. We present evidence that in the context of the TSE MCPIP1, so far known for its endonuclease activity toward mRNAs specified by distinct stem-loop (SL) structures, also suppresses translation...
February 19, 2018: Nucleic Acids Research
Jun-Seob Kim, Allen B Schantz, Sooyeon Song, Manish Kumar, Thomas K Wood
GhoT is a bacterial toxin of the type V toxin/antitoxin system that allows Escherichia coli to reduce its metabolism in response to oxidative and bile stress. GhoT functions by increasing membrane permeability and reducing both ATP levels and the proton motive force. However, how GhoT damages the inner membrane has not been elucidated. Here we investigated how GhoT damages membranes by studying its interaction with lipid bilayers and determined that GhoT does not cause macroscopic disruption of the lipid bilayer to increase membrane permeability to the dye carboxyfluorescein...
February 19, 2018: Biochemical and Biophysical Research Communications
Gang Wang, Zsigmond Varga, Jennifer Hofmann, Isidro E Zarraga, James W Swan
Reversible self-association of therapeutic antibodies is a key factor in high protein solution viscosities. In the present work, a coarse-grained computational model accounting for electrostatic, dispersion and long-ranged hydrodynamic interactions of two model monoclonal antibodies is applied to understand the nature of self-association, predicting the solution micro-structure and resulting transport properties of the solution. For the proteins investigated, the structure factor across a range of solution conditions shows quantitative agreement with neutron scattering experiments...
February 22, 2018: Journal of Physical Chemistry. B
Gao Qian, Li Yan-Wei, Huang Wen-Ling, Zhao Qin-Ping, Dong Hui-Fen
OBJECTIVE: To identify a myeloid differentiation factor 88 (MyD88) in Oncomelania hupensis , and characterize the role of MyD88 against Schistosoma japonicum infection. METHODS: The complete cDNA of MyD88 in O. hupensis was obtained by using rapid amplification of cDNA ends (RACE), and homologues sequences and conserved domains were aligned and the structure of MyD88 was predicted either. A phylogenetic tree of MyD88 was further constructed with other species. In addition, the mRNA expression level of O...
March 1, 2017: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
Tejinder Kaur Marwaha, Ashwini Madgulkar, Mangesh Bhalekar, Kalyani Asgaonkar
In pharmaceutical research drug discovery and development process is time-consuming and expensive. In many cases, it produces incompetent results due to the failure of in vitro and in vivo conventional approaches. Before any new drug is placed in the market it must undergo rigorous testing to get FDA approval. Due to the several limitations imposed by the drug discovery process, in recent times in silico approaches are widely applied in this field. In this review we have compiled docking studies which has found it's applications to predict drug excipient interactions which in turn assist to increase protein stability; to determine enzyme peptide interactions which maybe further used in drug development studies; to determine the most stable drug inclusion complex; to analyze structure at molecular level that ascertain an increase in solubility, dissolution and in turn the bioavailability of the drug; to design a dosage form that amplify the drug discovery and development process...
February 18, 2018: Current Drug Discovery Technologies
Dan Wang, Lin Zhang, JunFeng Hu, Dianshuai Gao, Xin Liu, Yan Sha
Lipases are physiologically important and ubiquitous enzymes that share a conserved domain and are classified into eight different families based on their amino acid sequences and fundamental biological properties. The Lipase3 family of lipases was reported to possess a canonical fold typical of α/β hydrolases and a typical catalytic triad, suggesting a distinct evolutionary origin for this family. Genes in the Lipase3 family do not have the same functions, but maintain the conserved Lipase3 domain. There have been extensive studies of Lipase3 structures and functions, but little is known about their evolutionary histories...
February 22, 2018: Genetica
Mohamed A Attia, Cassandra E Nelson, Wendy A Offen, Namrata Jain, Gideon J Davies, Jeffrey G Gardner, Harry Brumer
Background: Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte Cellvibrio japonicus has emerged as a genetically tractable model system to study biomass saccharification, in part due to its innate capacity to utilize a wide range of plant polysaccharides for growth...
2018: Biotechnology for Biofuels
Edward A Kiegle, Alex Garden, Elia Lacchini, Martin M Kater
Alternative splicing (AS) is a key modulator of development in many eukaryotic organisms. In plants, alternative splice forms of non-coding RNAs (ncRNAs) are known to modulate flowering time in Arabidopsis and fertility in rice. Here we demonstrate that alternative splicing of coding and long non-coding RNAs occurs during rice seed development by comparing AS in immature seeds vs. embryo and endosperm of mature seeds. Based on computational predictions of AS events determined from a Bayesian analysis of junction counts of RNA-seq datasets, differential splicing of protein-coding, and non-coding RNAs was determined...
2018: Frontiers in Plant Science
Ming-Xing Lu, Dan-Dan Pan, Jing Xu, Yang Liu, Gui-Rong Wang, Yu-Zhou Du
Aquaporins are integral membrane proteins some of which form high capacity water-selective channels, promoting water permeation across cell membranes. In this study, we isolated the aquaporin transcript ( Cs Drip1) of Chilo suppressalis , one of the important rice pests. Cs Drip1 included two variants, Cs Drip1_v1 and Cs Drip1_v2. Although Cs Drip1_v2 sequence (>409 bp) was longer than Cs Drip1_v1, they possessed the same open reading frame (ORF). Protein structure and topology of Cs Drip1 was analyzed using a predicted model, and the results demonstrated the conserved properties of insect water-specific aquaporins, including 6 transmembrane domains, 2 NPA motifs, ar/R constriction region (Phe69 , His194 , Ser203 , and Arg209 ) and the C-terminal peptide sequence ending in "SYDF...
2018: Frontiers in Physiology
Robert Lindroos, Matthijs C Dorst, Kai Du, Marko Filipović, Daniel Keller, Maya Ketzef, Alexander K Kozlov, Arvind Kumar, Mikael Lindahl, Anu G Nair, Juan Pérez-Fernández, Sten Grillner, Gilad Silberberg, Jeanette Hellgren Kotaleski
The basal ganglia are involved in the motivational and habitual control of motor and cognitive behaviors. Striatum, the largest basal ganglia input stage, integrates cortical and thalamic inputs in functionally segregated cortico-basal ganglia-thalamic loops, and in addition the basal ganglia output nuclei control targets in the brainstem. Striatal function depends on the balance between the direct pathway medium spiny neurons (D1-MSNs) that express D1 dopamine receptors and the indirect pathway MSNs that express D2 dopamine receptors...
2018: Frontiers in Neural Circuits
Mahiuddin Ahmed, Andres Lopez-Albaitero, Dmitry Pankov, Brian H Santich, Hong Liu, Su Yan, Jingyi Xiang, Pei Wang, Aisha N Hasan, Annamalai Selvakumar, Richard J O'Reilly, Cheng Liu, Nai-Kong V Cheung
EBV infection is associated with a number of malignancies of clinical unmet need, including Hodgkin lymphoma, nasopharyngeal carcinoma, gastric cancer, and posttransplant lymphoproliferative disease (PTLD), all of which express the EBV protein latent membrane protein 2A (LMP2A), an antigen that is difficult to target by conventional antibody approaches. To overcome this, we utilized phage display technology and a structure-guided selection strategy to generate human T cell receptor-like (TCR-like) monoclonal antibodies with exquisite specificity for the LMP2A-derived nonamer peptide, C426LGGLLTMV434 (CLG), as presented on HLA-A*02:01...
February 22, 2018: JCI Insight
Emrah Altindis, Weikang Cai, Masaji Sakaguchi, Fa Zhang, Wang GuoXiao, Fa Liu, Pierre De Meyts, Vasily Gelfanov, Hui Pan, Richard DiMarchi, C Ronald Kahn
Viruses are the most abundant biological entities and carry a wide variety of genetic material, including the ability to encode host-like proteins. Here we show that viruses carry sequences with significant homology to several human peptide hormones including insulin, insulin-like growth factors (IGF)-1 and -2, FGF-19 and -21, endothelin-1, inhibin, adiponectin, and resistin. Among the strongest homologies were those for four viral insulin/IGF-1-like peptides (VILPs), each encoded by a different member of the family Iridoviridae VILPs show up to 50% homology to human insulin/IGF-1, contain all critical cysteine residues, and are predicted to form similar 3D structures...
February 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
Fei Zhang, Minghui Wang, Jianing Xi, Jianghong Yang, Ao Li
An enduring challenge in personalized medicine lies in selecting a suitable drug for each individual patient. Here we concentrate on predicting drug responses based on a cohort of genomic, chemical structure, and target information. Therefore, a recently study such as GDSC has provided an unprecedented opportunity to infer the potential relationships between cell line and drug. While existing approach rely primarily on regression, classification or multiple kernel learning to predict drug responses. Synthetic approach indicates drug target and protein-protein interaction could have the potential to improve the prediction performance of drug response...
February 20, 2018: Scientific Reports
Kayley H Janssen, Manisha R Diaz, Matthew Golden, Justin W Graham, Wes Sanders, Matthew C Wolfgang, Timothy L Yahr
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen with distinct acute and chronic virulence phenotypes. Whereas acute virulence is typically associated with expression of a type III secretion system (T3SS), chronic virulence is characterized by biofilm formation. Many of the phenotypes associated with acute and chronic virulence are inversely regulated by RsmA and RsmF. RsmA and RsmF are both members of the CsrA family of RNA-binding proteins and regulate protein synthesis at the post-transcriptional level...
February 20, 2018: Journal of Bacteriology
Yaron Orenstein, Uwe Ohler, Bonnie Berger
BACKGROUND: RNA-binding proteins (RBPs) play vital roles in many processes in the cell. Different RBPs bind RNA with different sequence and structure specificities. While sequence specificities for a large set of 205 RBPs have been reported through the RNAcompete compendium, structure specificities are known for only a small fraction. The main limitation lies in the design of the RNAcompete technology, which tests RBP binding against unstructured RNA probes, making it difficult to infer structural preferences from these data...
February 20, 2018: BMC Genomics
Josiane V Cruz, Moysés F A Neto, Luciane B Silva, Ryan da S Ramos, Josivan da S Costa, Davi S B Brasil, Cleison C Lobato, Glauber V da Costa, José Adolfo H M Bittencourt, Carlos H T P da Silva, Franco H A Leite, Cleydson B R Santos
The Protein Kinase Receptor type 2 (RIPK2) plays an important role in the pathogenesis of inflammatory diseases; it signals downstream of the NOD1 and NOD2 intracellular sensors and promotes a productive inflammatory response. However, excessive NOD2 signaling has been associated with various diseases, including sarcoidosis and inflammatory arthritis; the pharmacological inhibition of RIPK2 is an affinity strategy that demonstrates an increased expression of pro-inflammatory secretion activity. In this study, a pharmacophoric model based on the crystallographic pose of ponatinib, a potent RIPK2 inhibitor, and 30 other ones selected from the BindingDB repository database, was built...
February 18, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Darcy Ab Jones, Stefania Bertazzoni, Chala J Turo, Robert A Syme, James K Hane
Effector proteins are important virulence factors of fungal plant pathogens and their prediction largely relies on bioinformatic methods. In this review we outline the current methods for the prediction of fungal plant pathogenicity effector proteins. Some fungal effectors have been characterised and are represented by conserved motifs or in sequence repositories, however most fungal effectors do not generally exhibit high conservation of amino acid sequence. Therefore various predictive methods have been developed around: general properties, structure, position in the genomic landscape, and detection of mutations including repeat-induced point mutations and positive selection...
February 17, 2018: Current Opinion in Microbiology
Nan Zheng, Yu-Xuan Sun, Liang-Li Yang, Liang Wu, Muhammad Nadeem Abbas, Chen Chen, Jin Gao, Xiao-Kun Li, Chao-Liang Liu, Li-Shang Dai
The complete mitochondrial genome (mitogenome) of Biston marginata (Lepidoptera: Geometridae) was determined and annotated. The circular genome is 15,470 bp long and it contains the entire set of 37 genes usually present in lepidopteran mitogenomes. The nucleotide composition of the genome is highly A + T biased, accounting for 81.20%, with a slightly positive AT skewness (0.028), indicating the occurrence of more As than Ts, as found in other Geometridae species. Except for cox1 gene starts with non-canonical initial codon CGA, all protein-coding genes start with ATN codon...
February 17, 2018: International Journal of Biological Macromolecules
Jerome Golebiowski, Claire de March, Jeremie Topin, Hiroaki Matsunami, Gleb Novikov, Kentaro Ikegami, Elise Bruguera
Deciphering how an odorant activates an odorant receptor (OR) and how changes in specific OR residues affect its responsiveness are central to understanding how we smell. A joint approach combining site-directed mutagenesis and functional assays with computational modeling has been used to explore the signaling mechanics of OR7D4. In this OR, a genetic polymorphism affects our perception of androstenone. A total of 0.12 ms molecular simulations predicted that, similarly to observations from other G protein-coupled receptors with known experimental structures, an activation pathway connects the ligand and G protein binding site...
February 20, 2018: Angewandte Chemie
Saulo H P de Oliveira, Charlotte M Deane
Motivation: Recent advances in co-evolution techniques have made possible the accurate prediction of protein structures in the absence of a template. Here, we provide a general approach that further utilizes co- evolution constraints to generate better fragment libraries for fragment-based protein structure prediction. Results: We have compared five different fragment library generation programmes on three different data sets encompassing over 400 unique protein folds...
February 15, 2018: Bioinformatics
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