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Protein function prediction

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https://www.readbyqxmd.com/read/28645153/defective-mitochondrial-rna-processing-due-to-pnpt1-variants-causes-leigh-syndrome
#1
Sanna Matilainen, Christopher J Carroll, Uwe Richter, Liliya Euro, Max Pohjanpelto, Anders Paetau, Pirjo Isohanni, Anu Suomalainen
Leigh syndrome is a severe infantile encephalopathy with an exceptionally variable genetic background. We studied the exome of a child manifesting with Leigh syndrome at one month of age and progressing to death by the age of 2.4 years, and identified novel compound heterozygous variants in PNPT1, encoding the polynucleotide phosphorylase (PNPase). Expression of the wild type PNPT1 in the subject's myoblasts functionally complemented the defects, and the pathogenicity was further supported by structural predictions and protein and RNA analyses...
June 22, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28644197/preoperative-regional-maximal-removal-rate-of-technetium-99m-galactosyl-human-serum-albumin-is-correlated-with-liver-functional-parameters-but-did-not-predict-postoperative-morbidity
#2
Koichi Yano, Atsushi Nanashima, Yoshiro Fujii, Masahide Hiyoshi, Naoya Imamura, Takeomi Hamada, Yuki Tsuchimochi, Takashi Wada, Yoichi Mizutani, Toshinori Hirai
BACKGROUND: Recently, posthepatectomy complications have been predicted by advances of new liver functional parameters, and the technetium-99m-galactosyl human serum albumin (GSA) liver scintigraphy has been applied widely for this purpose. We evaluated the clinical significance of the regional maximal removal rate (GSA-Rmax) in patients with various liver diseases as predictors of posthepatectomy complications. PATIENTS AND METHODS: Between 2012 and March 2016, we examined 200 patients who underwent hepatectomy for liver and biliary diseases...
June 22, 2017: Nuclear Medicine Communications
https://www.readbyqxmd.com/read/28644092/single-and-multiple-cardiovascular-biomarkers-in-subjects-without-a-previous-cardiovascular-event
#3
Manan Pareek, Deepak L Bhatt, Muthiah Vaduganathan, Tor Biering-Sørensen, Arman Qamar, Axel Cp Diederichsen, Jacob Eifer Møller, Peter Hindersson, Margrét Leósdóttir, Martin Magnusson, Peter M Nilsson, Michael H Olsen
Aims To assess the incremental value of biomarkers, including N-terminal prohormone of brain natriuretic peptide (NT-proBNP), high-sensitivity troponin T (hs-TnT), high-sensitivity C-reactive protein (hs-CRP), interleukin-6 (IL-6), growth differentiation factor 15 (GDF-15), and procollagen type 1 N-terminal propeptide (P1NP), in predicting incident cardiovascular events and mortality among asymptomatic individuals from the general population, beyond traditional risk factors, including fasting glucose and renal function (cystatin C), medication use, and echocardiographic measures...
January 1, 2017: European Journal of Preventive Cardiology
https://www.readbyqxmd.com/read/28643192/on-the-kinetics-of-body-versus-end-evaporation-and-addition-of-supramolecular-polymers
#4
Nitin S Tiwari, Paul van der Schoot
The kinetics of the self-assembly of supramolecular polymers is dictated by how monomers, dimers, trimers etc., attach to and detach from each other. It is for this reasons that researchers have proposed a plethora of pathways to explain the kinetics of various self-assembling supramolecules, including sulfur, linear micelles, living polymers and protein fibrils. Recent observations hint at the importance of a hitherto ignored molecular aggregation pathway that we refer to as "body evaporation and addition"...
June 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/28643166/structural-disorder-in-plant-proteins-where-plasticity-meets-sessility
#5
REVIEW
Alejandra A Covarrubias, Cesar L Cuevas-Velazquez, Paulette S Romero-Pérez, David F Rendón-Luna, Caspar C C Chater
Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks...
June 22, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28643139/cysteamine-revisited-repair-of-arginine-to-cysteine-mutations
#6
REVIEW
L Gallego-Villar, L Hannibal, J Häberle, B Thöny, T Ben-Omran, G K Nasrallah, Al-N Dewik, W D Kruger, H J Blom
Cysteamine is a small aminothiol endogenously derived from coenzyme A degradation. For some decades, synthetic cysteamine has been employed for the treatment of cystinosis, and new uses of the drug continue to emerge. In this review, we discuss the role of cysteamine in cellular and extracellular homeostasis and focus on the potential use of aminothiols to reconstitute the function of proteins harboring arginine (Arg) to cysteine (Cys) mutations, via repair of the Cys residue into a moiety that introduces an amino group, as seen in basic amino acid residues Lys and Arg...
June 22, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/28642865/spinal-muscular-atrophy-from-defective-chaperoning-of-snrnp-assembly-to-neuromuscular-dysfunction
#7
REVIEW
Maia Lanfranco, Neville Vassallo, Ruben J Cauchi
Spinal Muscular Atrophy (SMA) is a neuromuscular disorder that results from decreased levels of the survival motor neuron (SMN) protein. SMN is part of a multiprotein complex that also includes Gemins 2-8 and Unrip. The SMN-Gemins complex cooperates with the protein arginine methyltransferase 5 (PRMT5) complex, whose constituents include WD45, PRMT5 and pICln. Both complexes function as molecular chaperones, interacting with and assisting in the assembly of an Sm protein core onto small nuclear RNAs (snRNAs) to generate small nuclear ribonucleoproteins (snRNPs), which are the operating components of the spliceosome...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28642848/mycobacterium-tuberculosis-glyceraldehyde-3-phosphate-dehydrogenase-gapdh-functions-as-a-receptor-for-human-lactoferrin
#8
Himanshu Malhotra, Anil Patidar, Vishant M Boradia, Rajender Kumar, Rakesh D Nimbalkar, Ajay Kumar, Zahid Gani, Rajbeer Kaur, Prabha Garg, Manoj Raje, Chaaya I Raje
Iron is crucial for the survival of living cells, particularly the human pathogen Mycobacterium tuberculosis (M.tb) which uses multiple strategies to acquire and store iron. M.tb synthesizes high affinity iron chelators (siderophores), these extract iron from host iron carrier proteins such as transferrin (Tf) and lactoferrin (Lf). Recent studies have revealed that M.tb may also relocate several housekeeping proteins to the cell surface for capture and internalization of host iron carrier protein transferrin...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28642844/role-of-bacterioferritin-ferritin-in-m-tuberculosis-pathogenesis-and-drug-resistance-a-future-perspective-by-interactomic-approach
#9
Divakar Sharma, Deepa Bisht
Tuberculosis is caused by Mycobacterium tuberculosis, one of the most successful and deadliest human pathogen. Aminoglycosides resistance leads to emergence of extremely drug resistant strains of M. tuberculosis. Iron is crucial for the biological functions of the cells. Iron assimilation, storage and their utilization is not only involved in pathogenesis but also in emergence of drug resistance strains. We previously reported that iron storing proteins (bacterioferritin and ferritin) were found to be overexpressed in aminoglycosides resistant isolates...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28642634/analysis-of-map-kinase-mpk4-mekk1-mkk-genes-of-carica-papaya-l-comparative-to-other-plant-homologues
#10
Muhammad Hanam Hamid, Lina Rozano, Wee Chien Yeong, Janna Ong Abdullah, Noor Baity Saidi
Mitogen-activated protein kinase 4 (MPK4) interacts with the (Mitogen-activated protein kinase kinase kinase 1) MEKK1/ Mitogenactivated protein kinase kinase 1 (MKK1)/ Mitogen-activated protein kinase kinase 2 (MKK2) complex to affect its function in plant development or against pathogen attacks. The KEGG (Kyoto Encyclopedia of Genes and Genomes) network analysis of Arabidopsis thaliana revealed close interactions between those four genes in the same plant-pathogen interaction pathway, which warrants further study of these genes due to their evolutionary conservation in different plant species...
2017: Bioinformation
https://www.readbyqxmd.com/read/28642491/a-cross-species-approach-to-identify-transcriptional-regulators-exemplified-for-dnajc22-and-hnf4a
#11
A C Aschenbrenner, K Bassler, M Brondolin, L Bonaguro, P Carrera, K Klee, T Ulas, J L Schultze, M Hoch
There is an enormous need to make better use of the ever increasing wealth of publicly available genomic information and to utilize the tremendous progress in computational approaches in the life sciences. Transcriptional regulation of protein-coding genes is a major mechanism of controlling cellular functions. However, the myriad of transcription factors potentially controlling transcription of any given gene makes it often difficult to quickly identify the biological relevant transcription factors. Here, we report on the identification of Hnf4a as a major transcription factor of the so far unstudied DnaJ heat shock protein family (Hsp40) member C22 (Dnajc22)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642470/quantitative-proteomics-analysis-reveals-novel-targets-of-mir-21-in-zebrafish-embryos
#12
Ying Wu, Qi-Yong Lou, Feng Ge, Qian Xiong
MicroRNAs (miRNAs) are noncoding RNAs which control gene expression by the suppression of translation or the degradation of mRNAs. Dre-miR-21 (miR-21) has been reported to impact cardiac valvulogenesis in zebrafish embryos. However, the target genes of miR-21 are still largely unknown. Here a tandem isobaric mass tag (TMT)-based quantitative proteomic strategy was employed to identify the global profile of miR-21-regulated proteins. A total of 251 proteins were dysregulated after miR-21 knockdown, suggesting that they may be regulated by miR-21...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642038/functional-characterization-of-21-allelic-variants-of-dihydropyrimidinase
#13
Eiji Hishinuma, Fumika Akai, Yoko Narita, Masamitsu Maekawa, Hiroaki Yamaguchi, Nariyasu Mano, Akifumi Oda, Noriyasu Hirasawa, Masahiro Hiratsuka
Dihydropyrimidinase (DHP, EC 3.5.2.2), encoded by the gene DPYS, is the second enzyme in the catabolic pathway of pyrimidine and of fluoropyrimidine drugs such as 5-fluorouracil, which are commonly used in anticancer treatment; DHP catalyzes the hydrolytic ring opening of dihydrouracil and dihydro-5-fluorouracil. DPYS mutations are known to contribute to interindividual variations in the toxicity of fluoropyrimidine drugs, but the functional characterization of DHP allelic variants remains inadequate. In this study, in vitro analysis was performed on 22 allelic variants of DHP by transiently expressing wild-type DHP and 21 DHP variants in 293FT cells and characterizing their enzymatic activities by using dihydrouracil and dihydro-5-fluorouracil as substrates...
June 19, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28641555/supervised-machine-learning-methods-applied-to-predict-ligand-binding-affinity
#14
Gabriela Sehnem Heck, Val Oliveira Pintro, Richard Rene Pereira, Mauricio Boff de Ávila, Nayara Maria Bernhardt Levin, Walter Filgueira de Azevedo
BACKGROUND: Calculation of ligand-binding affinity is an open problem in computational medicinal chemistry. The ability to computationally predict affinities has a beneficial impact in the early stages of drug development, since it allows a mathematical model to assess protein-ligand interactions. Due to the availability of structural and binding information, machine learning methods have been applied to generate scoring functions with good predictive power. OBJECTIVE: Our goal here is to review recent developments in the application of machine learning methods to predict ligand- binding affinity...
June 22, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28641482/insights-into-eukaryotic-evolution-from-transmembrane-domain-lengths
#15
Aditya Mittal, Snigdha Singh
Biological membranes, comprised of proteins anchored by their trans-membrane domains (TMDs) creating a semi-permeable phase with lipid constituents, serve as "checkposts" for not only intracellular trafficking in eukaryotic cells but also for material transactions of all living cells with external environments. Hydropathy (or hydrophobicity) plots of "bitopic" proteins (i.e. having single alpha-helical TMDs) are routinely utilized in biochemistry texts for predicting their TMDs. The number of amino acids (i...
June 22, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28641268/newgoa-predicting-new-go-annotations-of-proteins-by-bi-random-walks-on-a-hybrid-graph
#16
Guoxian Yu, Guangyuan Fu, Jun Wang, Yingwen Zhao
A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many of them are incomplete. We proposed a method called NewGOA to predict new Gene Ontology (GO) annotations for incompletely annotated proteins and for completely un-annotated ones. NewGOA employs a hybrid graph, composed of two types of nodes (proteins and GO terms), to encode interactions between proteins, hierarchical relationships between terms and available annotations of proteins...
June 15, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28641136/age-exacerbates-abnormal-protein-expression-in-a-mouse-model-of-down-syndrome
#17
Md Mahiuddin Ahmed, Aaron Block, Suhong Tong, Muriel T Davisson, Katheleen J Gardiner
The Ts65Dn is a popular mouse model of Down syndrome (DS). It displays DS-relevant features of learning/memory deficits and age-related loss of functional markers in basal forebrain cholinergic neurons. Here we describe protein expression abnormalities in brain regions of 12-month-old male Ts65Dn mice. We show that the magnitudes of abnormalities of human chromosome 21 and non-human chromosome 21 orthologous proteins are greater at 12 months than at ∼6 months. Age-related exacerbations involve the number of components affected in the mechanistic target of rapamycin pathway, the levels of components of the mitogen-activated protein kinase pathway, and proteins associated with Alzheimer's disease...
May 10, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28640808/transmembrane-helical-interactions-in-the-cftr-channel-pore
#18
Jhuma Das, Andrei A Aleksandrov, Liying Cui, Lihua He, John R Riordan, Nikolay V Dokholyan
Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene affect CFTR protein biogenesis or its function as a chloride channel, resulting in dysregulation of epithelial fluid transport in the lung, pancreas and other organs in cystic fibrosis (CF). Development of pharmaceutical strategies to treat CF requires understanding of the mechanisms underlying channel function. However, incomplete 3D structural information on the unique ABC ion channel, CFTR, hinders elucidation of its functional mechanism and correction of cystic fibrosis causing mutants...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28639915/high-expression-of-tig3-predicts-poor-survival-in-patients-with-primary-glioblastoma
#19
Hongxiang Wang, Hanchong Xu, Tao Xu, Cong Tan, Mei Jiang, Yihong Chen, Xinyu Hu, Jinxu Zhou, Junyan Shen, Rong Qin, Daiyu Hu, Qilin Huang, Min Wang, Lian Wang, Dongxia Duan, Yong Yan, Juxiang Chen
TIG3 (tazarotene-induced gene 3) has been reported to suppress the progression of several malignancies, where this gene is universally downregulated. However, the expression of TIG3 in primary glioblastoma and its relevance to patient's prognosis have not been elaborated. Thus, this study was aimed to evaluate TIG3 expression level in primary glioblastoma and investigate the prognostic value of TIG3 for patients. The Cancer Genome Atlas database was first utilized to analyze the expression and prognostic potential of TIG3 in 528 glioblastoma cases...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28638922/-palmitoylation-of-heat-shock-protein-90-in-mouse-sperm
#20
Rui Li, Kun Li, Yue Yang, Pei-Bei Sun, Ai-Jun Chen, Ya Ni
Protein palmitoylation, one of post-translation modifications, refers to the addition of saturated 16-carbon palmitic acid to cysteine residues via the thioester bond. It plays key roles in various functional activities, such as the interaction, stability and location of proteins. Heat shock protein 90 (Hsp90), an important molecular chaperone, has been reported to be involved in sperm capacitation. However, it remains unclear whether protein palmitoylation exists in sperm and whether Hsp90 in sperm is palmitoylated under different physiological conditions...
June 25, 2017: Sheng Li Xue Bao: [Acta Physiologica Sinica]
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