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Protein function prediction

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https://www.readbyqxmd.com/read/29792307/putative-vaccine-candidates-and-drug-targets-identified-by-reverse-vaccinology-and-subtractive-genomics-approaches-to-control-haemophilus-ducreyi-the-causative-agent-of-chancroid
#1
Alissa de Sarom, Arun Kumar Jaiswal, Sandeep Tiwari, Letícia de Castro Oliveira, Debmalya Barh, Vasco Azevedo, Carlo Jose Oliveira, Siomar de Castro Soares
Chancroid is a sexually transmitted infection (STI) caused by the Gram-negative bacterium Haemophilus ducreyi The control of chancroid is difficult and the only current available treatment is antibiotic therapy; however, antibiotic resistance has been reported in endemic areas. Owing to recent outbreaks of STIs worldwide, it is important to keep searching for new treatment strategies and preventive measures. Here, we applied reverse vaccinology and subtractive genomic approaches for the in silico prediction of potential vaccine and drug targets against 28 strains of H...
May 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29792165/molecular-characterization-and-differential-expression-suggested-diverse-functions-of-p-type-ii-ca-2-atpases-in-triticum-aestivum-l
#2
Mehak Taneja, Santosh Kumar Upadhyay
BACKGROUND: Plant P-type II Ca2+ ATPases are formed by two distinct groups of proteins (ACAs and ECAs) that perform pumping of Ca2+ outside the cytoplasm during homeostasis, and play vital functions during development and stress management. In the present study, we have performed identification and characterisation of P-type II Ca 2+ ATPase gene family in an important crop plant Triticum aestivum. RESULTS: Herein, a total of 33 TaACA and 9 TaECA proteins were identified from the various chromosomes and sub-genomes of Triticum aestivum...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29791871/network-based-disease-module-discovery-by-a-novel-seed-connector-algorithm-with-pathobiological-implications
#3
Rui-Sheng Wang, Joseph Loscalzo
Understanding the genetic basis of complex diseases is challenging. Prior work shows that disease-related proteins do not typically function in isolation. Rather, they often interact with each other to form a network module that underlies dysfunctional mechanistic pathways. Identifying such disease modules will provide insights into a systems-level understanding of molecular mechanisms of diseases. Owing to the incompleteness of our knowledge of disease proteins and limited information on the biological mediators of pathobiological processes, the key proteins (seed proteins) for many diseases appear scattered over the human protein-protein interactome and form a few small branches, rather than coherent network modules...
May 20, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29791454/development-and-validation-of-a-short-food-questionnaire-to-screen-for-low-protein-intake-in-community-dwelling-older-adults-the-protein-screener-55-pro55
#4
Hanneke A H Wijnhoven, Liset E M Elstgeest, Henrica C W de Vet, Mary Nicolaou, Marieke B Snijder, Marjolein Visser
In old age, sufficient protein intake is important to preserve muscle mass and function. Around 50% of older adults (65+ y) consumes ≤1.0 g/kg adjusted body weight (BW)/day (d). There is no rapid method available to screen for low protein intake in old age. Therefore, we aimed to develop and validate a short food questionnaire to screen for low protein intake in community-dwelling older adults. We used data of 1348 older men and women (56-101 y) of the LASA study (the Netherlands) to develop the questionnaire and data of 563 older men and women (55-71 y) of the HELIUS study (the Netherlands) for external validation...
2018: PloS One
https://www.readbyqxmd.com/read/29790629/long-non-coding-rna-neat1-promoted-ovarian-cancer-cells-metastasis-via-regulating-of-mir-382-3p-rock1-axial
#5
Yangcheng Liu, Yong Wang, Xinming Fu, Zhi Lu
Long non-coding RNAs (lncRNAs) are extensively involved in various malignant tumors including ovarian cancer (OC). In the present study, we focused on the expression and function of nuclear enriched abundant transcript 1 (NEAT1) work on ovarian cancer cells' metastasis. We demonstrated that NEAT1 was up-regulated in OC tissue specimens and cell lines. Also, we revealed that depression of NEAT1 inhibited OC cells' metastasis and the expression of Rho associated coiled-coil containing protein kinase 1 (ROCK1) which was a metastasis-related gene...
May 23, 2018: Cancer Science
https://www.readbyqxmd.com/read/29790601/a-method-for-partitioning-the-information-contained-in-a-protein-sequence-between-its-structure-and-function
#6
Andrea Possenti, Michele Vendruscolo, Carlo Camilloni, Guido Tiana
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance between the amount of information supplied by the sequence and that left after that the protein has folded into its structure. We study the amount of information necessary to specify the protein structure, providing an estimate that keeps into account the thermodynamic properties of protein folding...
May 23, 2018: Proteins
https://www.readbyqxmd.com/read/29789900/associations-of-sensitive-cardiac-troponin-i-with-left-ventricular-morphology-function-and-prognosis-in-end-stage-renal-disease-patients-with-preserved-ejection-fraction
#7
Kenichiro Otsuka, Koki Nakanishi, Kenei Shimada, Haruo Nakamura, Hitoshi Inanami, Hiroki Nishioka, Kohei Fujimoto, Noriaki Kasayuki, Minoru Yoshiyama
Sensitive cardiac troponin I (cTnI) predicts all-cause and cardiovascular mortality in various clinical settings. However, its clinical significance in hemodialysis (HD) patients with preserved left ventricular ejection fraction (LVEF) has not been fully elucidated. This study investigated the association of cTnI with LV morphology and function, and its long-term outcome in HD patients with preserved LVEF. This prospective study consists of 96 HD patients with preserved LVEF (69 ± 8 years and 63% male) who underwent two-dimensional echocardiographic examination and biomarker tests including cTnI, brain natriuretic peptide, and high-sensitive C-reactive protein...
May 22, 2018: Heart and Vessels
https://www.readbyqxmd.com/read/29789713/upregulation-of-the-long-noncoding-rna-foxd2-as1-promotes-carcinogenesis-by-epigenetically-silencing-ephb3-through-ezh2-and-lsd1-and-predicts-poor-prognosis-in-gastric-cancer
#8
Tong-Peng Xu, Wen-Yu Wang, Pei Ma, You Shuai, Kun Zhao, Yan-Fen Wang, Wei Li, Rui Xia, Wen-Ming Chen, Er-Bao Zhang, Yong-Qian Shu
Accumulating data indicate that long noncoding RNAs (lncRNAs) serve as important modulators in biological processes and are dysregulated in diverse tumors. The function of FOXD2-AS1 in gastric cancer (GC) progression and related biological mechanisms remain undefined. A comprehensive analysis identified that FOXD2-AS1 enrichment was upregulated markedly in GC and positively correlated with a large tumor size, a later pathologic stage, and a poor prognosis. Gene-set enrichment analysis (GSEA) in GEO datasets uncovered that cell cycle and DNA replication associated genes were enriched in patients with high FOXD2-AS1 expression...
May 23, 2018: Oncogene
https://www.readbyqxmd.com/read/29789577/long-non-coding-rna-gm2199-rescues-liver-injury-and-promotes-hepatocyte-proliferation-through-the-upregulation-of-erk1-2
#9
Qiang Gao, Yunyan Gu, Yanan Jiang, Li Fan, Zixiang Wei, Haobin Jin, Xirui Yang, Lijuan Wang, Xuguang Li, Sheng Tai, Baofeng Yang, Yan Liu
Long non-coding RNAs (lncRNAs) are a new class of regulators of various human diseases. This study was designed to explore the potential role of lncRNAs in experimental hepatic damage. In vivo hepatic damage in mice and in vitro hepatocyte damage in AML12 and NCTC1469 cells were induced by carbon tetrachloride (CCl4 ) treatments. Expression profiles of lncRNAs and mRNAs were analyzed by microarray. Bioinformatics analyses were conducted to predict the potential functions of differentially expressed lncRNAs with respect to hepatic damage...
May 22, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29789355/hdl-functionality-and-cardiovascular-outcome-among-non-dialysis-chronic-kidney-disease-patients
#10
Kathrin Untersteller, Sabine Meissl, Markus Trieb, Insa Emrich, Adam Zawada, Michael Holzer, Eva Knuplez, Danilo Fliser, Gunnar Heine, Gunther Marsche
Cardiovascular disease remains the leading cause of morbidity and mortality in patients with chronic kidney disease (CKD). CKD profoundly affects high-density lipoprotein (HDL) composition and functionality, but if abnormal HDL independently contributes to cardiovascular events in CKD patients remains elusive. In the present study, we assessed whether compositional and functional properties of HDL predict cardiovascular outcome among 526 non-dialysis CKD patients who participate in the CARE FOR HOMe study. We measured HDL cholesterol, the content of HDL-associated pro-inflammatory serum amyloid A (SAA) and activities of the HDL enzymes paraoxonase and lipoprotein associated phospholipase A2 (Lp-PLA2)...
May 22, 2018: Journal of Lipid Research
https://www.readbyqxmd.com/read/29789326/hepatocellular-carcinoma-outcome-is-predicted-by-expression-of-neuronal-calcium-sensor-1
#11
Daniel Schuette, Lauren M Moore, Marie E Robert, Tamar H Taddei, Barbara E Ehrlich
BACKGROUND: Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related death worldwide. There is an urgent demand for prognostic biomarkers that facilitate early tumor detection, as the incidence of HCC has tripled in the USA in the last three decades. Biomarkers to identify populations at risk would have significant impact on survival. We recently found that expression of Neuronal Calcium Sensor 1 (NCS1), a Ca2+-dependent signaling molecule, predicted disease outcome in breast cancer, but its predictive value in other cancer types is unknown...
May 22, 2018: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/29788456/kinact-a-computational-approach-for-predicting-activating-missense-mutations-in-protein-kinases
#12
Carlos H M Rodrigues, David B Ascher, Douglas E V Pires
Protein phosphorylation is tightly regulated due to its vital role in many cellular processes. While gain of function mutations leading to constitutive activation of protein kinases are known to be driver events of many cancers, the identification of these mutations has proven challenging. Here we present Kinact, a novel machine learning approach for predicting kinase activating missense mutations using information from sequence and structure. By adapting our graph-based signatures, Kinact represents both structural and sequence information, which are used as evidence to train predictive models...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788292/biological-processes-modulating-longevity-across-primates-a-phylogenetic-genome-phenome-analysis
#13
Gerard Muntané, Xavier Farré, Juan Antonio Rodríguez, Cinta Pegueroles, David A Hughes, João Pedro de Magalhães, Toni Gabaldón, Arcadi Navarro
Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan (MLS) across primate species...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29788276/proteomic-analysis-and-prediction-of-amino-acid-variations-that-influence-protein-posttranslational-modifications
#14
Shaoping Shi, Lina Wang, Man Cao, Guodong Chen, Jialin Yu
Accumulative studies have indicated that amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence protein posttranslational modifications (PTMs) and bring about a detrimental effect on protein function. Computational mutation analysis can greatly narrow down the efforts on experimental work. To increase the utilization of current computational resources, we first provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis...
May 17, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29788092/cytokine-il9-triggers-the-pathogenesis-of-inflammatory-bowel-disease-through-the-mir21-cldn8-pathway
#15
Li Li, Shanshan Huang, Huiling Wang, Kang Chao, Li Ding, Rui Feng, Yun Qiu, Ting Feng, Gaoshi Zhou, Ji-Fan Hu, Minhu Chen, Shenghong Zhang
Background: Cytokine interleukin-9 (IL9) plays an essential role in the pathogenesis of inflammatory bowel disease. However, the molecular mechanism underlying the IL9 pathway remains unknown. Here, we initiate a series of studies to characterize the essential components of this pathway. Methods: The expression of IL9 in colon biopsies from Crohn's disease (CD) and controls were examined by quantitative polymerase chain reaction, immunoblot, and immunohistochemistry...
May 16, 2018: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/29787920/identification-and-characterization-of-chemosensory-genes-in-the-antennal-transcriptome-of-spodoptera-exigua
#16
Li-Xiao Du, Yang Liu, Jin Zhang, Xi-Wu Gao, Bing Wang, Gui-Rong Wang
Chemical senses are crucial for insect behaviors such as host preference, mate choice and oviposition site selection. Various protein families are involved in these processes, including odorant receptors (ORs), ionotropic receptors (IRs), gustatory receptors (GRs), chemosensory proteins (CSPs), odorant binding proteins (OBPs) and sensory neuron membrane proteins (SNMPs). To better understand the olfactory mechanism in Spodoptera exigua, we conducted transcriptome analysis of adult antennae and identified a total of 157 candidate chemosensory genes encoding 51 ORs, 20 IRs, 7 GRs, 32 CSPs, 45 OBPs and 2 SNMPs...
May 7, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29787733/the-major-outer-membrane-protein-of-legionella-pneumophila-lpg1974-shows-pore-forming-characteristics-similar-to-the-human-mitochondrial-outer-membrane-pore-hvdac1
#17
Farhan Younas, Nafiseh Soltanmohammadi, Oliver Knapp, Roland Benz
Legionella pneumophila is an aerobic and nonspore-forming pathogenic Gram-negative bacterium of the genus Legionella. It is the causative agent of Legionnaires' disease, also known as Legionellosis. The hosts of this organism are diverse, ranging from simple water borne protozoans such as amoebae to more complex hosts such as macrophages in humans. Genome analyses have shown the presence of genes coding for eukaryotic like proteins in several Legionella species. The presence of these proteins may assist L. pneumophila in its adaptation to the eukaryotic host...
May 19, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29787249/structure-function-relationships-in-the-oligomeric-nadph-dependent-assimilatory-sulfite-reductase
#18
Isabel Askenasy, Daniel Murray, Rachel M Andrews, Vladimir N Uversky, Huan He, M Elizabeth Stroupe
The central step in the assimilation of sulfur is a six-electron reduction of sulfite to sulfide, catalyzed by the oxidoreductase NADPH-dependent assimilatory Sulfite Reductase (SiR). SiR is composed of two subunits. One is a multi-domain flavin-binding reductase (SiRFP) and the other an iron-containing oxidase (SiRHP). Both enzymes are primarily globular, as expected from their functions as redox enzymes. Consequently, we know a fair amount about their structures but not how they assemble. Curiously, both structures have conspicuous regions that are structurally undefined, leaving questions about their functions and raising the possibility that they are critical in forming the larger complex...
May 22, 2018: Biochemistry
https://www.readbyqxmd.com/read/29786560/microfabrication-of-liver-and-heart-tissues-for-drug-development
#19
REVIEW
Grace E Brown, Salman R Khetani
Drug-induced liver- and cardiotoxicity remain among the leading causes of preclinical and clinical drug attrition, marketplace drug withdrawals and black-box warnings on marketed drugs. Unfortunately, animal testing has proven to be insufficient for accurately predicting drug-induced liver- and cardiotoxicity across many drug classes, likely due to significant differences in tissue functions across species. Thus, the field of in vitro human tissue engineering has gained increasing importance over the last 10 years...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29786430/galaxygpcrloop-template-based-and-ab-initio-structure-sampling-of-the-extracellular-loops-of-g-protein-coupled-receptors
#20
Jonghun Won, Gyu Rie Lee, Hahnbeom Park, Chaok Seok
The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed...
May 22, 2018: Journal of Chemical Information and Modeling
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