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Protein function prediction

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https://www.readbyqxmd.com/read/28750499/exosomal-mir-9-3p-suppresses-hbgf-5-expression-and-is-a-functional-biomarker-in-hepatocellular-carcinoma
#1
Jie Tang, Yun Li, Kai Liu, Qian Zhu, Wei-Hua Yang, Liang-Kun Xiong, De-Liang Guo
BACKGROUND: Hepatocellular carcinoma (HCC) is the fifth most common cancer and the third leading cause of cancer-related death worldwide. Exosomes are secreted membrane vesicles that play important roles in various diseases by transporting proteins and RNAs, including microRNAs, between cells. However, the function of exosomal miRNA in HCC has not been fully investigated. METHODS: Exosomes were obtained from the sera by ultracentrifugation and were processed for transmission electron microscopy (TEM)...
July 27, 2017: Minerva Medica
https://www.readbyqxmd.com/read/28750104/breps-2-0-optimization-of-sequence-pattern-prediction-for-enzyme-annotation
#2
Christian-Alexander Dudek, Henning Dannheim, Dietmar Schomburg
The prediction of gene functions is crucial for a large number of different life science areas. Faster high throughput sequencing techniques generate more and larger datasets. The manual annotation by classical wet-lab experiments is not suitable for these large amounts of data. We showed earlier that the automatic sequence pattern-based BrEPS protocol, based on manually curated sequences, can be used for the prediction of enzymatic functions of genes. The growing sequence databases provide the opportunity for more reliable patterns, but are also a challenge for the implementation of automatic protocols...
2017: PloS One
https://www.readbyqxmd.com/read/28750054/assisted-design-of-antibody-and-protein-therapeutics-adapt
#3
Victor Vivcharuk, Jason Baardsnes, Christophe Deprez, Traian Sulea, Maria Jaramillo, Christopher R Corbeil, Alaka Mullick, Joanne Magoon, Anne Marcil, Yves Durocher, Maureen D O'Connor-McCourt, Enrico O Purisima
Effective biologic therapeutics require binding affinities that are fine-tuned to their disease-related molecular target. The ADAPT (Assisted Design of Antibody and Protein Therapeutics) platform aids in the selection of mutants that improve/modulate the affinity of antibodies and other biologics. It uses a consensus z-score from three scoring functions and interleaves computational predictions with experimental validation, significantly enhancing the robustness of the design and selection of mutants. The platform was tested on three antibody Fab-antigen systems that spanned a wide range of initial binding affinities: bH1-VEGF-A (44 nM), bH1-HER2 (3...
2017: PloS One
https://www.readbyqxmd.com/read/28749997/difficulties-and-flaws-in-performing-accurate-determinations-of-zeta-potentials-of-metal-nanoparticles-in-complex-solutions-four-case-studies
#4
Sara Skoglund, Jonas Hedberg, Elena Yunda, Anna Godymchuk, Eva Blomberg, Inger Odnevall Wallinder
The zeta potential (ZP) is a parameter commonly used to characterize metal nanoparticles (NPs) in solution. Such determinations are for example performed in nanotoxicology since the ZP influences e.g. the interaction between cells and different biomolecules. Four case studies on different metal NPs (Cu and Zn NPs, and citrate capped Ag NPs) are presented in this study in order to provide guidance on how to accurately interpret and report ZP data. Solutions of high ionic strength (150 mM NaCl) induce a higher extent of particle agglomeration (elucidated with Ag NPs) when compared with conditions in 10 mM NaCl, which further complicates the prediction of the ZP due to e...
2017: PloS One
https://www.readbyqxmd.com/read/28749969/topologynet-topology-based-deep-convolutional-and-multi-task-neural-networks-for-biomolecular-property-predictions
#5
Zixuan Cang, Guowei Wei
Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the geometric and biological complexity. To address this problem we introduce the element-specific persistent homology (ESPH) method. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains important biological information via a multichannel image-like representation...
July 27, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28749740/the-role-of-high-sensitivity-c-reactive-protein-levels-in-functional-outcomes-in-patients-with-large-artery-atherosclerosis-and-small-artery-occlusion
#6
Dongzhe Hou, Ji Liu, Ren Feng, Yuan Gao, Yajing Wang, Jialing Wu
BACKGROUND: High-sensitivity C-reactive protein (hs-CRP) is an inflammatory marker that is associated with the outcomes of ischemic stroke. However, the role of hs-CRP levels in the functional outcomes after large-artery atherosclerosis (LAA) and small-artery occlusion (SAO) is poorly understood. METHODS: We recruited 1299 patients diagnosed as having LAA and 453 patients diagnosed as having SAO from 1 January 2009 to 31 December 2013, from the Department of Neurology, Tianjin Huanhu Hospital...
July 27, 2017: Neurological Research
https://www.readbyqxmd.com/read/28749677/nature-inspired-construction-of-two-dimensionally-self-assembled-peptide-on-pristine-graphene
#7
Young Hyun No, Nam Hyeong Kim, Bramaramba Gnapareddy, Bumjoon Choi, Yong-Tae Kim, Sreekantha Reddy Dugasani, One-Sun Lee, Kook-Han Kim, Young-Seon Ko, Seungwoo Lee, Sang Woo Lee, Sung Ha Park, Kilho Eom, Yong Ho Kim
Peptide assemblies have received significant attention because of their important role in biology and applications in bionanotechnology. Despite recent efforts to elucidate the principles of peptide self-assembly for developing novel functional devices, peptide self-assembly on two-dimensional nanomaterials has remained challenging. Here, we report nature-inspired two-dimensional peptide self-assembly on pristine graphene via optimization of peptide-peptide and peptide-graphene interactions. Two-dimensional peptide self-assembly was designed based on statistical analyses of >104 protein structures existing in nature and atomistic simulation-based structure predictions...
July 27, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28749324/investigation-of-the-fim1-putative-pilus-locus-of-streptococcus-equi-subspecies-equi
#8
Karen Frances Steward, Carl Robinson, Duncan J Maskell, Chiara Nenci, Andrew Stephen Waller
The Gram-positive bacterium Streptococcus equi subspecies equi (S. equi) is the causative agent of strangles, among the most frequently diagnosed infectious diseases of horses worldwide. Genome analysis of S. equi strain 4047 (Se4047) identified a putative operon, Fim1, with similarity to the pilus loci of other Gram-positive bacteria. The Fim1 locus was present in all strains of S. equi and its close relative S. equi subspecies zooepidemicus (S. zooepidemicus) that have been studied to date. In this study we provide evidence that the putative structural pilus proteins, SEQ_0936 and CNE, are produced on the cell surface during in vitro growth and in vivo infection...
July 28, 2017: Microbiology
https://www.readbyqxmd.com/read/28748912/a-novel-allosteric-site-in-casein-kinase-2%C3%AE-discovered-using-combining-bioinformatics-and-biochemistry-methods
#9
Hai-Ming Jiang, Jiang-Kai Dong, Kun Song, Tong-Dan Wang, Wen-Kang Huang, Jing-Miao Zhang, Xiu-Yan Yang, Ying Shen, Jian Zhang
Casein kinase 2 (CK2) is a highly pleiotropic serine-threonine kinase, which catalyzed phosphorylation of more than 300 proteins that are implicated in regulation of many cellular functions, such as signal transduction, transcriptional control, apoptosis and the cell cycle. On the other hand, CK2 is abnormally elevated in a variety of tumors, and is considered as a promising therapeutic target. The currently available ATP-competitive CK2 inhibitors, however, lack selectivity, which has impeded their development in cancer therapy...
July 27, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/28747908/unraveling-rubisco-form-i-and-form-ii-regulation-in-an-uncultured-organism-from-a-deep-sea-hydrothermal-vent-via-metagenomic-and-mutagenesis-studies
#10
Stefanie Böhnke, Mirjam Perner
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) catalyzes the first major step of carbon fixation in the Calvin-Benson-Bassham (CBB) cycle. This autotrophic CO2 fixation cycle accounts for almost all the assimilated carbon on Earth. Due to the primary role that RubisCO plays in autotrophic carbon fixation, it is important to understand how its gene expression is regulated and the enzyme is activated. Since the majority of all microorganisms are currently not culturable, we used a metagenomic approach to identify genes and enzymes associated with RubisCO expression...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28747718/predicting-the-functional-consequences-of-non-synonymous-single-nucleotide-polymorphisms-in-il8-gene
#11
Tikam Chand Dakal, Deepak Kala, Gourav Dhiman, Vinod Yadav, Andrey Krokhotin, Nikolay V Dokholyan
Here we report an in-silico approach for identification, characterization and validation of deleterious non-synonymous SNPs (nsSNPs) in the interleukin-8 gene using three steps. In first step, sequence homology-based genetic analysis of a set of 50 coding SNPs associated with 41 rsIDs using SIFT (Sorting Intolerant from Tolerant) and PROVEAN (Protein Variation Effect Analyzer) identified 23 nsSNPs to be putatively damaging/deleterious in at least one of the two tools used. Subsequently, structure-homology based PolyPhen-2 (Polymorphism Phenotyping) analysis predicted 9 of 23 nsSNPs (K4T, E31A, E31K, S41Y, I55N, P59L, P59S, L70P and V88D) to be damaging...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747564/high-eg5-expression-predicts-poor-prognosis-in-breast-cancer
#12
Qin Jin, Fang Huang, Xudong Wang, Huijun Zhu, Yun Xian, Jieying Li, Shu Zhang, Qichao Ni
Eg5 is a motor protein belonging to the kinesin-5 family and has been suggested to exert important function in tumors. In this study, we determined the mRNA and protein expression levels of Eg5 in cancerous and non-cancerous breast tissue by quantitative real-time polymerase chain reaction (qRT-PCR) and tissue microarray immunohistochemistry analysis (TMA-IHC) respectively. The results of 20 fresh-frozen BC samples demonstrated that Eg5 mRNA levels were significantly higher in BC tissues compared with corresponding non-cancerous tissue (p = 0...
July 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28747553/krt8-upregulation-promotes-tumor-metastasis-and-is-predictive-of-a-poor-prognosis-in-clear-cell-renal-cell-carcinoma
#13
Hai-Song Tan, Wei-Hua Jiang, Yi He, De-Sheng Wang, Zhen-Jie Wu, Deng-Shuang Wu, Li Gao, Yi Bao, Jia-Zi Shi, Bing Liu, Li-Jun Ma, Lin-Hui Wang
Keratin 8 (KRT8) plays an essential role in the development and metastasis of multiple human cancers. However, its role in clear cell renal cell carcinoma (ccRCC) remains unexplored. Here, we investigated the expression pattern, clinical significance, and function of KRT8 in ccRCC. KRT8 mRNA and protein levels were determined in two large cohorts using quantitative real-time polymerase chain reaction (qRT-PCR) and tissue microarray (TMA) immunohistochemistry (IHC), respectively. We found that KRT8 expression was upregulated in ccRCC and vein tumor thrombi (VTTs)...
July 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/28747448/movement-disorder-in-gnao1-encephalopathy-associated-with-gain-of-function-mutations
#14
Huijie Feng, Benita Sjögren, Behirda Karaj, Vincent Shaw, Aysegul Gezer, Richard R Neubig
OBJECTIVE: To define molecular mechanisms underlying the clinical spectrum of epilepsy and movement disorder in individuals with de novo mutations in the GNAO1 gene. METHODS: We identified all GNAO1 mutations reported in individuals with epilepsy (early infantile epileptiform encephalopathy 17) or movement disorders through April 2016; 15 de novo mutant alleles from 25 individuals were introduced into the Gαo subunit by site-directed mutagenesis in a mammalian expression plasmid...
July 26, 2017: Neurology
https://www.readbyqxmd.com/read/28747311/an-n-terminal-pfs230-domain-produced-in-baculovirus-as-a-biological-active-transmission-blocking-vaccine-candidate
#15
Shwu-Maan Lee, Chia-Kuei Wu, Jordan L Plieskatt, Kazutoyo Miura, John M Hickey, C Richter King
Transmission-blocking vaccines have the potential to accelerate malaria parasite elimination by inducing antibodies that block parasite transmission from humans to mosquitoes. Pfs230, a gametocyte surface protein involved in gamete function, has long been a promising candidate. Due to the large size (3,135 amino acids), complex domains, and repeating six-cysteine (6-Cys) motifs with a multitude of disulfide bonds, the feasibility of expression of a full-length protein has been difficult. A priority focus, therefore, has been on the generation of single domains, including N-terminal fragments...
July 26, 2017: Clinical and Vaccine Immunology: CVI
https://www.readbyqxmd.com/read/28747241/developing-a-predictive-model-for-the-energy-content-of-goat-milk-as-the-basis-for-a-functional-unit-formulation-to-be-used-in-the-life-cycle-assessment-of-dairy-goat-production-systems
#16
P P Danieli, B Ronchi
Recent reports on livestock environmental impact based on life cycle assessment (LCA) did not fully consider the case of the dairy goat. Assignment of an environmental impact (e.g. global warming potential) to a specific product needs to be related to the appropriate 'unitary amount' or functional unit (FU). For milk, the energy content may provide a common basis for a definition of the FU. To date, no ad hoc formulations for the FU of goat milk have been proposed. For these reasons, this study aimed to develop and test one or more predictive models (DPMs) for the gross energy (GE) content of goat milk, based on published compositional data, such as fat (F), protein, total solids (TS), solid non-fat matter (SNF), lactose (Lac) and ash...
July 27, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28747184/meg2-is-regulated-by-mir-181a-5p-and-functions-as-a-tumour-suppressor-gene-to-suppress-the-proliferation-and-migration-of-gastric-cancer-cells
#17
Zhijian Liu, Feng Sun, Yeting Hong, Yanqing Liu, Min Fen, Kai Yin, Xiaolong Ge, Feng Wang, Xi Chen, Wenxian Guan
BACKGROUND: Protein-tyrosine phosphatase MEG2 (MEG2) is a classic tyrosine-specific protein tyrosine phosphatase (PTP). It has been reported that MEG2 participates in the carcinogenesis of the breast and liver. However, functions of MEG2 in gastric cancer remain poorly understood. METHODS: We examined the expression of MEG2 protein by western blotting and that of miR-181a-5p by qRT-PCR. We used bioinformatic analyses to search for miRNAs that potentially target MEG2...
July 26, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28746940/comparison-of-the-skin-penetration-of-3-metabolically-stable-chemicals-using-fresh-and-frozen-human-skin
#18
Carine Jacques-Jamin, Hélène Duplan, Helga Rothe, Ophelie Vaillant, Joan Eilstein, Sebastien Grégoire, Richard Cubberley, Daniela Lange, Corie Ellison, Martina Klaric, Nicola Hewitt, Andreas Schepky
BACKGROUND: The Cosmetics Europe ADME Task Force is developing in vitro and in silico tools for predicting skin and systemic concentrations after topical application of cosmetic ingredients. There are conflicting reports as to whether the freezing process affects the penetration of chemicals; therefore, we evaluated whether the storage of human skin used in our studies (8-12 weeks at -20°C) affected the penetration of model chemicals. METHODS: Finite doses of trans-cinnamic acid (TCA), benzoic acid (BA), and 6-methylcoumarin (6MC) (non-volatile, non-protein reactive and metabolically stable in skin) were applied to fresh and thawed frozen skin from the same donors...
July 27, 2017: Skin Pharmacology and Physiology
https://www.readbyqxmd.com/read/28746368/the-genome-wide-identification-and-transcriptional-levels-of-dna-methyltransferases-and-demethylases-in-globe-artichoke
#19
Silvia Gianoglio, Andrea Moglia, Alberto Acquadro, Cinzia Comino, Ezio Portis
Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases) and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1), CMT (chromomethyltransferases) and DRM (domains rearranged methyltransferases). Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var...
2017: PloS One
https://www.readbyqxmd.com/read/28746350/differential-effects-of-n-linked-glycosylation-of-vstm5-at-multiple-sites-on-surface-expression-and-filopodia-formation
#20
A-Ram Lee, Sulgi Kim, Kwang Woo Ko, Chul-Seung Park
V-set and transmembrane domain-containing protein 5 (Vstm5), a newly characterized small membrane glycoprotein, can induce membrane protrusions in various cells. Vstm5 can modulate both the position and complexity of central neurons by altering their membrane morphology and dynamics. In this study, we investigated the significance of glycosylation in the expression and function of Vstm5. Four N-linked glycosylation sites (Asn43, Asn87, Asn101, and Asn108) are predicted to be located in the extracellular N-terminus of mouse Vstm5...
2017: PloS One
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