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Protein function prediction

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https://www.readbyqxmd.com/read/29331417/down-regulation-of-rip3-potentiates-cisplatin-chemoresistance-by-triggering-hsp90-erk-pathway-mediated-dna-repair-in-esophageal-squamous-cell-carcinoma
#1
Yulin Sun, Linhui Zhai, Shouzhi Ma, Chengpu Zhang, Lina Zhao, Ning Li, Yang Xu, Tao Zhang, Zhimin Guo, Heng Zhang, Ping Xu, Xiaohang Zhao
Receptor interacting protein kinase 3 (RIP3) is a critical regulator of programmed necrotic cell death. Here, we observed that RIP3 was significantly down-regulated in esophageal cancer. And its remaining expression was associated with better response to chemotherapy and prolonged survival. Notably, re-expression of kinase-dead RIP3 also restored cisplatin sensitivity, suggesting that some roles of RIP3 beyond necroptosis may be involved in cisplatin-based chemosensitivity. To investigate the mechanisms, a large-scale quantitative proteomics study was performed after cisplatin treatment in RIP3-knockdown cells...
January 10, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29331201/impact-of-polymer-geometry-on-the-interactions-of-protein-peg-conjugates
#2
Jonathan Zarzar, Whitney Shatz, Nikhil Peer, Rosalynn Taing, Brian McGarry, Yun Liu, Daniel G Greene, Isidro E Zarraga
The conjugation of high molecular weight polyethylene glycol (PEG) to an active pharmaceutical ingredient (API) is an attractive strategy for the modification of biophysical and biodistribution properties of the API. Indeed, several therapeutic proteins conjugated to PEG have been safely administered in the clinic. While there have been studies on the configuration of these conjugates in solution, investigations on the impact of PEG geometry on protein-PEG conjugate interactions is limited. In this study, we use dynamic light scattering (DLS), rheology, and small-angle neutron scattering (SANS) to investigate the biophysical solution and interaction behavior of a 50kDa Fab protein attached to either a linear or tetrameric (branched) 40kDa PEG molecule...
November 8, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/29331136/zwitterionization-of-glycine-in-water-environment-stabilization-mechanism-and-nmr-spectral-signatures
#3
Danillo Valverde, Zélia Maria da Costa Ludwig, Célia Regina da Costa, Valdemir Ludwig, Herbert C Georg
At physiological conditions, myriads of biomolecules (e.g., amino acids, peptides, and proteins) exist predominantly in the zwitterionic structural form and their biological functions will result in these conditions. However these geometrical structures are inaccessible energetically in the gas phase, and at this point, stabilization of amino-acids in physiological conditions is still under debate. In this paper, the electronic properties of a glycine molecule in the liquid environment were studied by performing a relaxation of the glycine geometry in liquid water using the free energy gradient method combined with a sequential quantum mechanics/molecular mechanics approach...
January 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29331040/jun-gal-cd74-and-c1qb-as-potential-indicator-for-neuropathic-pain
#4
Ji-An Yang, Jun-Min He, Jing-Min Lu, Li-Juan Ji
Neuropathic pain is a kind of pain caused by primary or secondary impairment or dysfunction of peripheral or central nervous system. Patients with neuropathic pain were often with poor clinical outcome. We screened the differentially expressed genes between sciatic nerve injury and dorsal root ganglion gene in the sham operation model. Microarray and the spared nerve injury module were used to explore the molecular mechanism of neuropathic pain by injuries and the differentially expressed genes (DEGs) were identified out...
January 13, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29330536/carbon-limitation-drives-gc-content-evolution-of-a-marine-bacterium-in-an-individual-based-genome-scale-model
#5
Ferdi L Hellweger, Yongjie Huang, Haiwei Luo
An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model...
January 12, 2018: ISME Journal
https://www.readbyqxmd.com/read/29330521/rgs7-is-recurrently-mutated-in-melanoma-and-promotes-migration-and-invasion-of-human-cancer-cells
#6
Nouar Qutob, Ikuo Masuho, Michal Alon, Rafi Emmanuel, Isadora Cohen, Antonella Di Pizio, Jason Madore, Abdel Elkahloun, Tamar Ziv, Ronen Levy, Jared J Gartner, Victoria K Hill, Jimmy C Lin, Yael Hevroni, Polina Greenberg, Alexandra Brodezki, Steven A Rosenberg, Mickey Kosloff, Nicholas K Hayward, Arie Admon, Masha Y Niv, Richard A Scolyer, Kirill A Martemyanov, Yardena Samuels
Analysis of 501 melanoma exomes revealed RGS7, which encodes a GTPase-accelerating protein (GAP), to be a tumor-suppressor gene. RGS7 was mutated in 11% of melanomas and was found to harbor three recurrent mutations (p.R44C, p.E383K and p.R416Q). Structural modeling of the most common recurrent mutation of the three (p.R44C) predicted that it destabilizes the protein due to the loss of an H-bond and salt bridge network between the mutated position and the serine and aspartic acid residues at positions 58 as 61, respectively...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330500/integration-of-gwas-pathway-and-network-analyses-reveals-novel-mechanistic-insights-into-the-synthesis-of-milk-proteins-in-dairy-cows
#7
Sara Pegolo, Núria Mach, Yuliaxis Ramayo-Caldas, Stefano Schiavon, Giovanni Bittante, Alessio Cecchinato
The quantities and proportions of protein fractions have notable effects on the nutritional and technological value of milk. Although much is known about the effects of genetic variants on milk proteins, the complex relationships among the set of genes and pathways regulating the different protein fractions synthesis and secretion into milk in dairy cows are still not completely understood. We conducted genome-wide association studies (GWAS) for milk nitrogen fractions in a cohort of 1,011 Brown Swiss cows, which uncovered 170 significant single nucleotide polymorphism (SNPs), mostly located on BTA6 and BTA11...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330189/targeted-synthesis-and-characterization-of-a-gene-cluster-encoding-nad-p-h-dependent-3%C3%AE-3%C3%AE-and-12%C3%AE-hydroxysteroid-dehydrogenases-from-eggerthella-cag-298-a-gut-metagenomic-sequence
#8
Sean M Mythen, Saravanan Devendran, Celia Méndez-García, Isaac Cann, Jason M Ridlon
Gut metagenomic sequences provide a rich source of microbial genes, the majority of which are annotated by homology or unknown. Genes and gene pathways that encode enzymes catalyzing biotransformation of host bile acids are important to identify in gut metagenomic sequences due to the importance of bile acids on gut microbiome structure and host physiology. Hydroxysteroid dehydrogenases (HSDH) are pyridine nucleotide-dependent enzymes with stereo-specificity and regio-specificity for bile acid and steroid hydroxyl groups...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29330128/exploiting-ion-channel-structure-to-assess-rare-variant-pathogenicity
#9
Brett M Kroncke, Tao Yang, Prince Kannankeril, M Benjamin Shoemaker, Dan M Roden
BACKGROUND: A 27-year-old female was seen for long QT syndrome. She was found to be a carrier of two variants, KCNQ1 Val162Met and KCNH2 Ser55Leu, and both were annotated as pathogenic by a diagnostic laboratory in part because of sequence proximity to other known pathogenic variants. OBJECTIVE: To assess the relationship between both the KCNQ1 and KCNH2 variants and clinical significance using protein structure, in vitro functional assays, and familial segregation...
January 9, 2018: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/29329531/chemical-genomic-guided-engineering-of-gamma-valerolactone-tolerant-yeast
#10
Scott Bottoms, Quinn Dickinson, Mick McGee, Li Hinchman, Alan Higbee, Alex Hebert, Jose Serate, Dan Xie, Yaoping Zhang, Joshua J Coon, Chad L Myers, Robert Landick, Jeff S Piotrowski
BACKGROUND: Gamma valerolactone (GVL) treatment of lignocellulosic bomass is a promising technology for degradation of biomass for biofuel production; however, GVL is toxic to fermentative microbes. Using a combination of chemical genomics with the yeast (Saccharomyces cerevisiae) deletion collection to identify sensitive and resistant mutants, and chemical proteomics to monitor protein abundance in the presence of GVL, we sought to understand the mechanism toxicity and resistance to GVL with the goal of engineering a GVL-tolerant, xylose-fermenting yeast...
January 12, 2018: Microbial Cell Factories
https://www.readbyqxmd.com/read/29329521/treating-c3-glomerulopathy-with-eculizumab
#11
Thomas Welte, Frederic Arnold, Julia Kappes, Maximilian Seidl, Karsten Häffner, Carsten Bergmann, Gerd Walz, Elke Neumann-Haefelin
BACKGROUND: C3 glomerulopathy (C3G) is a rare, but severe glomerular disease with grim prognosis. The complex pathogenesis is just unfolding, and involves acquired as well as inherited dysregulation of the alternative pathway of the complement cascade. Currently, there is no established therapy. Treatment with the C5 complement inhibitor eculizumab may be a therapeutic option. However, due to rarity of the disease, parameters predicting treatment response remain largely unknown. METHODS: Seven patients with C3G (five with C3 glomerulonephritis and two with dense deposit disease) were treated with eculizumab...
January 12, 2018: BMC Nephrology
https://www.readbyqxmd.com/read/29329425/comparison-of-hepatic-2d-sandwich-cultures-and-3d-spheroids-for-long-term-toxicity-applications-a-multi-center-study
#12
Catherine C Bell, Anita C A Dankers, Volker M Lauschke, Rowena Sison-Young, Roz Jenkins, Cliff Rowe, Chris Goldring, Kevin Park, Sophie Regan, Tracy Walker, Chris Schofield, Audrey Baze, Alison J Foster, Dominic Williams, Amy W M van de Ven, Frank Jacobs, Jos van Houdt, Tuula Lähteenmäki, Jan Snoeys, Satu Juhila, Lysiane Richert, Magnus Ingelman-Sundberg
Primary human hepatocytes (PHH) are commonly used for in vitro studies of drug-induced liver injury. However, when cultured as 2D monolayers, PHH lose crucial hepatic functions within hours. This dedifferentiation can be ameliorated when PHH are cultured in sandwich configuration (2Dsw), particularly when cultures are regularly re-overlaid with extracellular matrix, or as 3D spheroids. In this study, the six participating laboratories evaluated the robustness of these two model systems made from cryopreserved PHH from the same donors considering both inter-donor and inter-lab variability and compared their suitability for use in repeated-dose toxicity studies using 5 different hepatotoxins with different toxicity mechanisms...
January 10, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29329283/modeling-the-assembly-order-of-multimeric-heteroprotein-complexes
#13
Lenna X Peterson, Yoichiro Togawa, Juan Esquivel-Rodriguez, Genki Terashi, Charles Christoffer, Amitava Roy, Woong-Hee Shin, Daisuke Kihara
Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly...
January 12, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29328462/serum-and-glucocorticoid-regulated-kinase-1-sgk1-is-a-predictor-of-poor-prognosis-in-non-small-cell-lung-cancer-and-its-dynamic-pattern-following-treatment-with-sgk1-inhibitor-and-%C3%AE-ray-irradiation-was-elucidated
#14
Zhiyuan Tang, Qin Shen, Hao Xie, Zhu Zhou, Guanglin Shi, Caixin Zhang, Anaz Mohammed, Yi Wu, Songshi Ni, Xiaoyu Zhou
The tumor suppressor gene p53 and its dynamic patterns have caused widespread attention in the field of cancer research. Serum and glucocorticoid-regulated kinase 1 (SGK1) with features of serine/threonine kinase activity, which also contributes to the structural and functional similarities with the AKT family of kinases, is a key enzyme in the regulation of immune responses in tumor cells, and SGK1 was noted to be expressed in close relation to p53 protein levels, and there exists a negative feedback pathway between intracellular SGK1 and p53...
January 3, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29328442/identification-of-differentially-expressed-genes-and-regulatory-relationships-in-huntington-s-disease-by-bioinformatics-analysis
#15
Xiaoyu Dong, Shuyan Cong
Huntington's disease (HD) is an inherited, progressive neurodegenerative disease caused by a CAG expansion in the huntingtin (HTT) gene; various dysfunctions of biological processes in HD have been proposed. However, at present the exact pathogenesis of HD is not fully understood. The present study aimed to explore the pathogenesis of HD using a computational bioinformatics analysis of gene expression. GSE11358 was downloaded from the Gene Expression Omnibus andthe differentially expressed genes (DEGs) in the mutant HTT knock‑in cell model STHdhQ111/Q111 were predicted...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328435/mir%C3%A2-214-reduces-cisplatin-resistance-by-targeting-netrin%C3%A2-1-in-bladder-cancer-cells
#16
Jiao Liu, Jianbin Bi, Zeliang Li, Zhenhua Li, Xiankui Liu, Chuize Kong
miR‑214 has been reported to be downregulated in several cancer types, such as bladder cancer. However, its involvement in apoptosis and chemoresistance has not been investigated. The present study aimed to clarify the biological function of miR‑214 and potential mechanisms in chemoresistance of bladder cancer cells. Reverse transcription‑quantitative polymerase chain reaction demonstrated that miR‑214 was downregulated in bladder cancer tissues compared with the level in normal tissues. miR‑214 was downregulated in bladder cancer cell lines compared with the level in the normal cell line SV‑HUC‑1...
January 10, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29328431/bioinformatic-analysis-of-gene-expression-profiling-of-intracranial-aneurysm
#17
Lijuan Bo, Bo Wei, Zhanfeng Wang, Chaohui Li, Zheng Gao, Zhuang Miao
Intracranial aneurysm (IA) is a severe clinical condition of primary concern and currently, there is no effective therapeutic reagent. The present study aimed to investigate the molecular mechanism of IA via bioinformatic analysis. Various gene expression profiles (GSE26969) were downloaded from the Gene Expression Omnibus database, including 3 IA and 3 normal superficial temporal artery samples. Firstly, the limma package in R language was used to identify differentially expressed genes (DEGs; P‑value <0...
December 29, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328410/cldn5-affects-lncrnas-acting-as-cerna-dynamics-contributing-to-regulating-blood%C3%A2-brain-barrier-permeability-in-tumor-brain-metastasis
#18
Shun-Chang Ma, Qi Li, Jia-Yi Peng, Jian-Long Zhouwen, Dai-Nan Zhang, Chuan-Bao Zhang, Wen-Guo Jiang, Wang Jia
The blood‑brain barrier (BBB) constitutes an efficient organization of tight junctions that limits the delivery of tumor to the brain. The principal tight junction protein in BBB is claudin‑5 (CLDN5), but its mechanism of action remains largely unknown. Long non‑coding RNAs (lncRNAs) are aberrantly expressed in many cancers, some lncRNAs play key roles in regulating BBB permeability and are involved in tumor brain metastasis. In particular, lncRNAs can function as competing endogenous RNAs (ceRNAs). Herein, we investigated whether ceRNA dysregulation is associated with alterations of the level of CLDN5 in human brain vascular endothelial hCMEC/D3 cells...
January 10, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29328395/bioinformatic-identification-of-chemoresistance-associated-micrornas-in-breast-cancer-based-on-microarray-data
#19
Ya-Wen Wang, Weiguo Zhang, Rong Ma
Breast cancer is the most commonly diagnosed cancer among females, and chemoresistance constitutes a major clinical obstacle to the treatment of this disease. MicroRNAs (miRNAs) are related to human cancer development, progression and drug resistance. To identify breast cancer chemoresistance-associated miRNAs, miRNA microarray dataset GSE71142, including five chemoresistant breast cancer tissues and five chemosensitive tissues, was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DE-miRNAs) were obtained by t-test and the potential target genes were predicted by miRWalk2...
January 10, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29328377/feature-genes-in-metastatic-breast-cancer-identified-by-metade-and-svm-classifier-methods
#20
Youlin Tuo, Ning An, Ming Zhang
The aim of the present study was to investigate the feature genes in metastatic breast cancer samples. A total of 5 expression profiles of metastatic breast cancer samples were downloaded from the Gene Expression Omnibus database, which were then analyzed using the MetaQC and MetaDE packages in R language. The feature genes between metastasis and non‑metastasis samples were screened under the threshold of P<0.05. Based on the protein‑protein interactions (PPIs) in the Biological General Repository for Interaction Datasets, Human Protein Reference Database and Biomolecular Interaction Network Database, the PPI network of the feature genes was constructed...
January 9, 2018: Molecular Medicine Reports
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