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Protein function prediction

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https://www.readbyqxmd.com/read/28934823/comprehensive-analysis-of-non-synonymous-natural-variants-of-g-protein-coupled-receptors
#1
Hee Ryung Kim, Nguyen Minh Duc, Ka Young Chung
G protein-coupled receptors (GPCRs) are the largest superfamily of transmembrane receptors and have vital signaling functions in various organs. Because of their critical roles in physiology and pathology, GPCRs are the most commonly used therapeutic target. It has been suggested that GPCRs undergo massive genetic variations such as genetic polymorphisms and DNA insertions or deletions. Among these genetic variations, non-synonymous natural variations change the amino acid sequence and could thus alter GPCR functions such as expression, localization, signaling, and ligand binding, which may be involved in disease development and altered responses to GPCR-targeting drugs...
September 19, 2017: Biomolecules & Therapeutics
https://www.readbyqxmd.com/read/28934732/long-noncoding-rna-cir-promotes-chondrocyte-extracellular-matrix-degradation-in-osteoarthritis-by-acting-as-a-sponge-for-mir-27b
#2
Yu-Fei Li, Shu-Hua Li, Yong Liu, Ya-Tong Luo
BACKGROUND/AIMS: Osteoarthritis (OA) is a degenerative joint disease characterized by articular cartilage degradation. The degradation of the extracellular matrix (ECM) of chondrocyte is closely associated with the destruction of joints in OA patients. lncRNAs are non-coding segments of RNA that possess important regulatory functions at the cellular level and in a variety of pathophysiological processes. The present study was conducted to investigate whether lncRNA-CIR regulated the expression of MMP13 as a sponge of miR-27 in OA...
September 21, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28934693/enzyme-classification-using-multiclass-support-vector-machine-and-feature-subset-selection
#3
Debasmita Pradhan, Sudarsan Padhy, Biswajit Sahoo
Proteins are the macromolecules responsible for almost all biological processes in a cell. With the availability of large number of protein sequences from different sequencing projects, the challenge with the scientist is to characterize their functions. As the wet lab methods are time consuming and expensive, many computational methods such as FASTA, PSI-BLAST, DNA microarray clustering, and Nearest Neighborhood classification on protein-protein interaction network have been proposed. Support vector machine is one such method that has been used successfully for several problems such as protein fold recognition, protein structure prediction etc...
August 31, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28934548/controlling-styrene-maleic-acid-lipid-particles-through-raft
#4
Anton A A Smith, Henriette Elisabeth Autzen, Tomas Laursen, Vincent Wu, Max Yen, Aaron Hall, Scott D Hansen, Yifan Cheng, Ting Xu
The ability of styrene maleic acid copolymers to dissolve lipid membranes into nanosized lipid particles is a facile method of obtaining membrane proteins in solubilized lipid discs while conserving part of its native lipid environment. While the currently used copolymers can readily extract membrane proteins in native nanodiscs, their highly disperse composition is likely to influence the dispersity of the discs as well as the extraction efficiency. In this study, reversible addition fragmentation chain transfer was used to control the polymer architecture and dispersity of molecular weights with a high-precision...
September 21, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28934517/human-epididymis-protein-4-as-a-potential-biomarker-of-chronic-kidney-disease-in-female-patients-with-normal-ovarian-function
#5
Tengfei Yuan, Yan Li
Background: Elevated serum concentrations of human epididymis protein 4 (HE4) have appeared in a large number of female patients with chronic kidney disease (CKD). However, it is unknow whether HE4 could be a potential biomarker for diagnosis of CKD. Objective: To evaluate whether serum HE4 is a potential biomarker of CKD in our cohort of 238 ethnic Han Chinese female patients, between the ages of 19 and 89 years. Methods: We selected 230 healthy control individuals and 238 female patients with CKD for inclusion in our study...
August 1, 2017: Laboratory Medicine
https://www.readbyqxmd.com/read/28934503/a-novel-requirement-for-drosha-in-maintenance-of-mammalian-cg-methylation
#6
Athanasia Stathopoulou, Jyoti B Chhetri, John C Ambrose, Pierre-Olivier Estève, Lexiang Ji, Hediye Erdjument-Bromage, Guoqiang Zhang, Thomas A Neubert, Sriharsa Pradhan, Javier Herrero, Robert J Schmitz, Steen K T Ooi
In mammals, faithful inheritance of genomic methylation patterns ensures proper gene regulation and cell behaviour, impacting normal development and fertility. Following establishment, genomic methylation patterns are transmitted through S-phase by the maintenance methyltransferase Dnmt1. Using a protein interaction screen, we identify Microprocessor component DROSHA as a novel DNMT1-interactor. Drosha-deficient embryonic stem (ES) cells display genomic hypomethylation that is not accounted for by changes in the levels of DNMT proteins...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934487/supernalign-a-new-tool-for-flexible-superposition-of-homologous-rna-structures-and-inference-of-accurate-structure-based-sequence-alignments
#7
Pawel Piatkowski, Jagoda Jablonska, Adriana Zyla, Dorota Niedzialek, Dorota Matelska, Elzbieta Jankowska, Tomasz Walen, Wayne K Dawson, Janusz M Bujnicki
RNA has been found to play an ever-increasing role in a variety of biological processes. The function of most non-coding RNA molecules depends on their structure. Comparing and classifying macromolecular 3D structures is of crucial importance for structure-based function inference and it is used in the characterization of functional motifs and in structure prediction by comparative modeling. However, compared to the numerous methods for protein structure superposition, there are few tools dedicated to the superimposing of RNA 3D structures...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934323/identification-chromosomal-arrangements-and-expression-analyses-of-the-evolutionarily-conserved-prmt1-gene-in-chicken-in-comparison-with-its-vertebrate-paralogue-prmt8
#8
Yi-Chun Wang, Chien-Wen Wang, Wen-Chang Lin, Yun-Jung Tsai, Chien-Ping Chang, Yu-Jen Lee, Min-Jon Lin, Chuan Li
Nine protein arginine methyltransferases (PRMTs) are conserved in mammals and fish. Among these, PRMT1 is the major type I PRMT for asymmetric dimethylarginine (ADMA) formation and is the most conserved and widely distributed one. Two chicken prmt1 splicing variants were assembled and confirmed by RT-PCR experiments. However, only two scaffolds containing single separate prmt1 exon with high GC contents are present in the current chicken genome assembly. Besides, prmt1 exons are scattered in separate small scaffolds in most avian species...
2017: PloS One
https://www.readbyqxmd.com/read/28934129/a-comprehensive-survey-of-the-roles-of-highly-disordered-proteins-in-type-2-diabetes
#9
Zhihua Du, Vladimir N Uversky
Type 2 diabetes mellitus (T2DM) is a chronic and progressive disease that is strongly associated with hyperglycemia (high blood sugar) related to either insulin resistance or insufficient insulin production. Among the various molecular events and players implicated in the manifestation and development of diabetes mellitus, proteins play several important roles. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database has information on 34 human proteins experimentally shown to be related to the T2DM pathogenesis...
September 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28933744/energy-and-protein-in-critically-ill-patients-with-aki-a-prospective-multicenter-observational-study-using-indirect-calorimetry-and-protein-catabolic-rate
#10
Alice Sabatino, Miriam Theilla, Moran Hellerman, Pierre Singer, Umberto Maggiore, Maria Barbagallo, Giuseppe Regolisti, Enrico Fiaccadori
The optimal nutritional support in Acute Kidney Injury (AKI) still remains an open issue. The present study was aimed at evaluating the validity of conventional predictive formulas for the calculation of both energy expenditure and protein needs in critically ill patients with AKI. A prospective, multicenter, observational study was conducted on adult patients hospitalized with AKI in three different intensive care units (ICU). Nutrient needs were estimated by different methods: the Guidelines of the European Society of Parenteral and Enteral Nutrition (ESPEN) for both calories and proteins, the Harris-Benedict equation, the Penn-State and Faisy-Fagon equations for energy...
July 26, 2017: Nutrients
https://www.readbyqxmd.com/read/28933593/dynein-promotes-porcine-oocyte-meiotic-progression-by-maintaining-cytoskeletal-structures-and-cortical-granule-arrangement
#11
Yilong Miao, Changyin Zhou, Zhaokang Cui, Liansheng Tang, Xiayan ShiYang, Yajuan Lu, Mianqun Zhang, Xiaoxin Dai, Bo Xiong
Cytoplasmic dynein is a family of cytoskeletal motor proteins that move towards the minus-end of the microtubules to perform functions in a variety of mitotic processes such as cargo transport, organelle positioning, chromosome movement and centrosome assembly. However, its specific roles during mammalian oocyte meiosis have not been fully defined. Herein, we investigated the critical events during porcine oocyte meiotic maturation after inhibition of dynein by Ciliobrevin D treatment. We found that oocyte meiotic progression was arrested when inhibited of dynein by showing the poor expansion of cumulus cells and decreased rate of polar body extrusion...
September 21, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28933084/-cloning-and-bioinformatics-analysis-of-1-hydroxy-2-methyl-2-e-butenyl-4-diphosphate-reductase%C3%AF-pchdr1%C3%AF-gene-in-phlegmarirus-carinatus
#12
Zhi-Li Zhang, Hai-Zhou Lv, Xu Guo, Liu He, Jing-Yuan Song, Chao Sun, Hong-Mei Luo
The open reading frame of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (HDR) was cloned from Phlegmarirus carinatus by RT-PCR method and the sequence was analyzed by bioinformatics tools. After searching the transcriptome dataset of P. carinatus, one unique sequence encoding 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase was discovered. The primers were designed according to the cDNA sequence of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase from the dataset. And then, the open reading frame (ORF) of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase, named as PcHDR1 (GenBank Accession number:JQ957845), was cloned by RT-PCR strategy with the template of mixed RNA extracted from roots, stem and leaf of P...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932761/digestion-of-peptidoglycan-and-analysis-of-soluble-fragments
#13
Ryan E Schaub, Joseph P Dillard
Peptidoglycan (murein) is a vital component of the cell wall of nearly all bacteria, composed of sugars linked by short peptides. This protocol describes the purification of macromolecular peptidoglycan from cultured bacteria and the analysis of enzyme-digested peptidoglycan fragments using high performance liquid chromatography (HPLC). Digested peptidoglycan fragments can be identified by mass spectrometry, or predicted by comparing retention times with other published chromatograms. The quantitative nature of this method allows for the measurement of changes to peptidoglycan composition between different species of bacteria, growth conditions, or mutations...
August 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28932706/global-proteomics-revealed-klebsiella-pneumoniae-induced-autophagy-and-oxidative-stress-in-caenorhabditis-elegans-by-inhibiting-pi3k-akt-mtor-pathway-during-infection
#14
Arumugam Kamaladevi, Krishnaswamy Balamurugan
The enterobacterium, Klebsiella pneumoniae invades the intestinal epithelium of humans by interfering with multiple host cell response. To uncover a system-level overview of host response during infection, we analyzed the global dynamics of protein profiling in Caenorhabditis elegans using quantitative proteomics approach. Comparison of protein samples of nematodes exposed to K. pneumoniae for 12, 24, and 36 h by 2DE revealed several changes in host proteome. A total of 266 host-encoded proteins were identified by 2DE MALDI-MS/MS and LC-MS/MS and the interacting partners of the identified proteins were predicted by STRING 10...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28932107/bioinformatics-study-of-m-9053g-a-mutation-at-the-atp6-gene-in-relation-to-type-2-diabetes-mellitus-and-cataract-diseases
#15
Iman Permana Maksum, Sandy Risfi Saputra, Nenden Indrayati, Muhammad Yusuf, Toto Subroto
The mitochondrial disease often associated with various illnesses in relation to the activity of cells metabolites and the synthesis of adenosine triphosphate (ATP), including alteration in the mitochondrial DNA. The mutation of m.9053G>A at the ATP6 gene was found in patients with type 2 diabetes mellitus (DM type 2) and cataract. Therefore, this mutation is predicted to be clinical features of the 2 diseases. ATP6 gene encodes protein subunit of ATPase6, a part of ATP synthase, which is important in the electron transfer and proton translocation in intracellular respiration system...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28931012/cbta-toxin-of-escherichia-coli-inhibits-cell-division-and-cell-elongation-via-direct-and-independent-interactions-with-ftsz-and-mreb
#16
Danielle M Heller, Mrinalini Tavag, Ann Hochschild
The toxin components of toxin-antitoxin modules, found in bacterial plasmids, phages, and chromosomes, typically target a single macromolecule to interfere with an essential cellular process. An apparent exception is the chromosomally encoded toxin component of the E. coli CbtA/CbeA toxin-antitoxin module, which can inhibit both cell division and cell elongation. A small protein of only 124 amino acids, CbtA, was previously proposed to interact with both FtsZ, a tubulin homolog that is essential for cell division, and MreB, an actin homolog that is essential for cell elongation...
September 20, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28929346/o-glcnac-dependent-regulation-of-progesterone-receptor-function-in-breast-cancer
#17
Gloria M Trinca, Merit L Goodman, Evangelia K Papachristou, Clive S D'Santos, Prabhakar Chalise, Rashna Madan, Chad Slawson, Christy R Hagan
Emerging clinical trial data implicate progestins in the development of breast cancer. While the role for the progesterone receptor (PR) in this process remains controversial, it is clear that PR, a steroid-activated nuclear receptor, alters the transcriptional landscape of breast cancer. PR interacts with many different types of proteins, including transcriptional co-activators and co-repressors, transcription factors, nuclear receptors, and proteins that post-translationally modify PR (i.e., kinases and phosphatases)...
September 19, 2017: Hormones & Cancer
https://www.readbyqxmd.com/read/28929019/heterologous-expression-of-plasmodium-vivax-apical-membrane-antigen-1-pvama1-for-binding-peptide-selection
#18
Ching Hoong Chew, Yvonne Ai Lian Lim, Kek Heng Chua
BACKGROUND: Plasmodium is an obligate intracellular parasite. Apical membrane antigen 1 (AMA1) is the most prominent and well characterized malarial surface antigen that is essential for parasite-host cell invasion, i.e., for sporozoite to invade and replicate within hepatocytes in the liver stage and merozoite to penetrate and replicate within erythrocytes in the blood stage. AMA1 has long served as a potent antimalarial drug target and is a pivotal vaccine candidate. A good understanding of the structure and molecular function of this Plasmodium protein, particularly its involvement in host-cell adhesion and invasion, is of great interest and hence it offers an attractive target for the development of novel therapeutics...
2017: PeerJ
https://www.readbyqxmd.com/read/28928950/using-sheep-genomes-from-diverse-u-s-breeds-to-identify-missense-variants-in-genes-affecting-fecundity
#19
Michael P Heaton, Timothy P L Smith, Bradley A Freking, Aspen M Workman, Gary L Bennett, Jacky K Carnahan, Theodore S Kalbfleisch
Background:  Access to sheep genome sequences significantly improves the chances of identifying genes that may influence the health, welfare, and productivity of these animals.   Methods:  A public, searchable DNA sequence resource for U.S. sheep was created with whole genome sequence (WGS) of 96 rams.  The animals shared minimal pedigree relationships and represent nine popular U.S. breeds and a composite line.  The genomes are viewable online with the user-friendly Integrated Genome Viewer environment, and may be used to identify and decode gene variants present in U...
2017: F1000Research
https://www.readbyqxmd.com/read/28928893/the-epigenetic-regulation-of-cxcl14-plays-a-role-in-the-pathobiology-of-oral-cancers
#20
Ryuji Nakayama, Kazumune Arikawa, Ujjal K Bhawal
Background: Chemokines selectively attract and activate leukocytes and play roles in a variety of homeostatic and disease processes. Explore the biological properties of CXCL14 seems complicated due to unknown functional characteristics of CXCL14 in cancer. Methods: To study the multistep process of oral cancer development, we analyzed oral samples spanning normalcy, dysplasia and cancer from multiple perspectives, revealing a cascade of progressive changes. Results: CXCL14 protein was expressed in the cytoplasm adjacent to tumors...
2017: Journal of Cancer
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