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Protein translation

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https://www.readbyqxmd.com/read/28227691/understanding-the-cochlear-implant-environment-by-mapping-perilymph-proteomes-from-different-species
#1
Jonathan C Palmer, Megan S Lord, Jeremy L Pinyon, Andrew K Wise, Nigel H Lovell, Paul M Carter, Ya Lang Enke, Gary D Housley, Rylie A Green, Jonathan C Palmer, Megan S Lord, Jeremy L Pinyon, Andrew K Wise, Nigel H Lovell, Paul M Carter, Ya Lang Enke, Gary D Housley, Rylie A Green, Ya Lang Enke, Rylie A Green, Jonathan C Palmer, Nigel H Lovell, Paul M Carter, Jeremy L Pinyon, Gary D Housley, Andrew K Wise, Megan S Lord
Cochlear implants operate within a bony channel of the cochlea, bathed in a fluid known as the perilymph. The perilymph is a complex fluid containing ions and proteins, which are known to actively interact with metallic electrodes. To improve our understanding of how cochlear implant performance varies in preclinical in vivo studies in comparison to human trials and patient outcomes, the protein composition (or perilymph proteome) is needed. Samples of perilymph were gathered from feline and guinea pig subjects and analyzed using liquid chromatography with tandem mass spectrometry (LC-MS/MS) to produce proteomes and compare against the recently published human proteome...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28225828/systematic-analysis-of-non-structural-protein-features-for-the-prediction-of-ptm-function-potential-by-artificial-neural-networks
#2
Henry M Dewhurst, Matthew P Torres
Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our knowledge of PTM functionality encompasses less than 5% of this data. We previously developed SAPH-ire (Structural Analysis of PTM Hotspots) for the prioritization of eukaryotic PTMs based on function potential of discrete modified alignment positions (MAPs) in a set of 8 protein families...
2017: PloS One
https://www.readbyqxmd.com/read/28225193/human-neural-progenitor-transplantation-rescues-behavior-and-reduces-%C3%AE-synuclein-in-a-transgenic-model-of-dementia-with-lewy-bodies
#3
Natalie R S Goldberg, Samuel E Marsh, Joseph Ochaba, Brandon C Shelley, Hayk Davtyan, Leslie M Thompson, Joan S Steffan, Clive N Svendsen, Mathew Blurton-Jones
Synucleinopathies are a group of neurodegenerative disorders sharing the common feature of misfolding and accumulation of the presynaptic protein α-synuclein (α-syn) into insoluble aggregates. Within this diverse group, Dementia with Lewy Bodies (DLB) is characterized by the aberrant accumulation of α-syn in cortical, hippocampal, and brainstem neurons, resulting in multiple cellular stressors that particularly impair dopamine and glutamate neurotransmission and related motor and cognitive function. Recent studies show that murine neural stem cell (NSC) transplantation can improve cognitive or motor function in transgenic models of Alzheimer's and Huntington's disease, and DLB...
February 22, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28224978/methylated-antibody-affinity-purification-to-improve-proteomic-identification-of-plant-rna-polymerase-pol-v-complex-and-the-interacting-proteins
#4
Guochen Qin, Jun Ma, Xiaomei Chen, Zhaoqing Chu, Yi-Min She
Affinity purification followed by enzymatic digestion and mass spectrometry has been widely utilized for the sensitive detection of interacting proteins and protein complexes in various organisms. In plants, the method is technically challenging due to the low abundance proteins, non-specific binding and difficulties of eluting interacting proteins from antibody beads. In this report, we describe a strategy to modify antibodies by reductive methylation of lysines without affecting their binding properties, followed by on-bead digestion of bound proteins with endoproteinase Lys-C...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224114/ha-triggers-the-switch-from-mek1-sumoylation-to-phosphorylation-of-the-erk-pathway-in-influenza-a-virus-infected-cells-and-facilitates-its-infection
#5
Chengmin Wang, Huimin Liu, Jing Luo, Lin Chen, Meng Li, Wen Su, Na Zhao, Shelan Liu, Li Xie, Yaxiong Jia, Hua Ding, Xiufeng Wan, Hongxuan He
Several post-translational modifications in host cells are hijacked by pathogens to facilitate their propagation. A number of components of the influenza virus have been reported to be modified by small ubiquitin-like modifier (SUMO) proteins during infection. We hypothesized that the MAPK/ERK pathway could be modified by SUMO1 because the SUMOylation of MEK1 was quickly eliminated after influenza A virus infection. We identified host cell MEK1 as a target of SUMO1 through LC/MS/MS, and enhanced MEK1 SUMOylation inhibited the infection of the virus, while inhibition of host cell MEK1 SUMOylation facilitated virus propagation...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28223523/rps3-us3-promotes-mrna-binding-at-the-40s-ribosome-entry-channel-and-stabilizes-preinitiation-complexes-at-start-codons
#6
Jinsheng Dong, Colin Echeverría Aitken, Anil Thakur, Byung-Sik Shin, Jon R Lorsch, Alan G Hinnebusch
The eukaryotic 43S preinitiation complex (PIC) bearing Met-tRNAi(Met) in a ternary complex (TC) with eukaryotic initiation factor (eIF)2-GTP scans the mRNA leader for an AUG codon in favorable "Kozak" context. AUG recognition provokes rearrangement from an open PIC conformation with TC bound in a state not fully engaged with the P site ("POUT") to a closed, arrested conformation with TC tightly bound in the "PIN" state. Yeast ribosomal protein Rps3/uS3 resides in the mRNA entry channel of the 40S subunit and contacts mRNA via conserved residues whose functional importance was unknown...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223409/asc1-hel2-and-slh1-couple-translation-arrest-to-nascent-chain-degradation
#7
Cole Stone Sitron, Joseph Hun Park, Onn Brandman
Premature arrest of protein synthesis within the open reading frame elicits a protective response that degrades the incomplete nascent chain. In this response, arrested 80S ribosomes are split into their large and small subunits, allowing assembly of the Ribosome Quality control Complex (RQC), which targets nascent chains for degradation. How the cell recognizes arrested nascent chains among the vast pool of actively translating polypeptides is poorly understood. We systematically examined translation arrest and modification of nascent chains in Saccharomyces cerevisiae to characterize the steps that couple arrest to RQC targeting...
February 21, 2017: RNA
https://www.readbyqxmd.com/read/28223408/inducing-circular-rna-formation-using-the-crispr-endoribonuclease-csy4
#8
Erin K Borchardt, Rita M Meganck, Heather A Vincent, Christopher B Ball, Silvia B V Ramos, Nathaniel J Moorman, William F Marzluff, Aravind Asokan
Circular RNAs (circRNAs) are highly stable, covalently closed RNAs that are regulated in a spatiotemporal manner and whose functions are largely unknown. These molecules have the potential to be incorporated into engineered systems with broad technological implications. Here we describe a switch for inducing backsplicing of an engineered circRNA that relies on the CRISPR endoribonuclease, Csy4, as an activator of circularization. The endoribonuclease activity and 3' end-stabilizing properties of Csy4 are particularly suited for this task...
February 21, 2017: RNA
https://www.readbyqxmd.com/read/28223358/structural-and-biochemical-analysis-of-escherichia-coli-obge-a-central-regulator-of-bacterial-persistence
#9
Sotirios Gkekas, Ranjan Kumar Singh, Alexander V Shkumatov, Joris Messens, Maarten Fauvart, Natalie Verstraeten, Jan Michiels, Wim Versées
The Obg protein family belongs to the TRAFAC (translation factor) class of P-loop GTPases and is conserved from bacteria to eukaryotes. Essential roles in many different cellular processes have been suggested for the Obg protein from Escherichia coli (ObgE), and we recently showed that it is a central regulator of bacterial persistence. Here, we report the first crystal structure of ObgE at 1.85 Å resolution in the GDP-bound state, showing the characteristic N-terminal domain and a central G domain that are common to all Obg proteins...
February 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28223315/the-focal-adhesion-targeting-fat-domain-of-p130-crk-associated-substrate-p130cas-confers-mechanosensing-function
#10
Peta M Bradbury, Kylie Turner, Camilla Mitchell, Kaitlyn R Griffin, Shiloh Middlemiss, Loretta Lau, Rebecca Dagg, Elena Taran, Justin Cooper-White, Ben Fabry, Geraldine M O'Neill
The Cas family of focal adhesion proteins contain a highly conserved C-terminal focal adhesion targeting (FAT) domain. To determine the role of the FAT domain we compared wildtype exogenous NEDD9 with a hybrid construct in which the NEDD9 FAT domain is exchanged for the p130Cas FAT domain. Fluorescence recovery after photobleaching (FRAP) revealed significantly slowed exchange of the fusion protein at focal adhesions and significantly slower 2D migration. No differences were detected in cell stiffness measured with Atomic Force Microscopy (AFM) and cell adhesion forces measured with a magnetic tweezer device...
February 21, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28223095/palmitoylation-of-plasmodium-alveolins-promotes-cytoskeletal-function
#11
Annie Z Tremp, Fatimah S Al-Khattaf, Johannes T Dessens
S-palmitoylation is a post-translational lipid modification that is widespread among Plasmodium proteins and essential for parasite development. Little is known about the contribution of palmitoylation to the function of individual parasite molecules and structures. Alveolins are major components of the subpellicular network (SPN), a cortical cytoskeleton primarily involved in providing mechanical strength to the cell. We show here that the alveolin IMC1c is palmitoylated on a conserved cysteine motif, and that non-palmitoylated IMC1c displays normal expression, stability and trafficking...
February 18, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28223055/plasma-monocyte-chemotactic-protein-1-is-associated-with-acute-kidney-injury-and-death-after-cardiac-operations
#12
Dennis G Moledina, Selin Isguven, Eric McArthur, Heather Thiessen-Philbrook, Amit X Garg, Michael Shlipak, Richard Whitlock, Peter A Kavsak, Steven G Coca, Chirag R Parikh
BACKGROUND: Monocyte chemotactic protein-1 (MCP-1; chemokine C-C ligand-2 [CCL-2]) is upregulated in ischemia-reperfusion injury and is a promising biomarker of inflammation in cardiac operations. METHODS: We measured preoperative and postoperative plasma MCP-1 levels in adults undergoing cardiac operations to evaluate the association of perioperative MCP-1 levels with acute kidney injury (AKI) and death in Translational Research Investigating Biomarker Endpoints in AKI (TRIBE-AKI), a prospective, multicenter, observational cohort...
February 18, 2017: Annals of Thoracic Surgery
https://www.readbyqxmd.com/read/28222887/rare-er-protein-misfolding-mistrafficking-disorders-therapeutic-developments
#13
REVIEW
Ramanath Narayana Hegde, Advait Subramanian, Prathyush Pothukuchi, Seetharaman Parashuraman, Alberto Luini
The presence of a functional protein at the appropriate location in the cell is the result of the processes of transcription, translation, folding and trafficking to the correct destination. There are numerous diseases that are caused by protein misfolding, mainly due to mutations in the respective gene. The consequences of this misfolding may be that proteins effectively lose their function, either by being removed by the cellular quality control machinery or by accumulating at the incorrect intracellular or extracellular location...
February 9, 2017: Tissue & Cell
https://www.readbyqxmd.com/read/28222786/post-translational-modification-of-parkin
#14
REVIEW
Joy Chakraborty, Valentina Basso, Elena Ziviani
: Mutations in the gene encoding for the E3 ubiquitin ligase Parkin are associated to a rare form of familiar autosomal recessive Parkinsonism. Despite decades of research on the Parkin protein, whose structure has been recently solved, little is known about the specific signalling pathways that lead to Parkin activation. Parkin activity spans from mitochondria quality control to tumor suppression and stress protection; it is thus tempting to hypothesize that the broad impact of Parkin on cellular physiology might be the result of different post translational modifications that can be controlled by balanced opposing events...
February 21, 2017: Biology Direct
https://www.readbyqxmd.com/read/28222748/identification-of-host-cellular-proteins-that-interact-with-the-m-protein-of-a-highly-pathogenic-porcine-reproductive-and-respiratory-syndrome-virus-vaccine-strain
#15
Qian Wang, Yanwei Li, Hong Dong, Li Wang, Jinmei Peng, Tongqing An, Xufu Yang, Zhijun Tian, Xuehui Cai
BACKGROUND: The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) continues to pose one of the greatest threats to the swine industry. M protein is the most conserved and important structural protein of PRRSV. However, information about the host cellular proteins that interact with M protein remains limited. METHODS: Host cellular proteins that interact with the M protein of HP-PRRSV were immunoprecipitated from MARC-145 cells infected with PRRSV HuN4-F112 using the M monoclonal antibody (mAb)...
February 22, 2017: Virology Journal
https://www.readbyqxmd.com/read/28222670/microrna-223-3p-inhibits-human-bladder-cancer-cell-migration-and-invasion
#16
Ju Guo, Runfu Cao, Xingwei Yu, Zewen Xiao, Zhiwen Chen
The regulation of initiation and progression during carcinogenesis of bladder carcinoma is not completely elucidated. Dysregulation of microRNAs has been detected to play critical roles in the development of various cancers, including bladder carcinoma, whereas the involvement of miR-223-3p in the tumorigenesis of bladder carcinoma has not been studied. Here, we show that significantly higher levels of nuclear receptor coactivator 1 and significantly lower levels of miR-223-3p were detected in bladder carcinoma tissue, compared to the adjacent non-tumor tissue...
February 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28222432/extracellular-hmgb1-modulates-glutamate-metabolism-associated-with-kainic-acid-induced-epilepsy-like-hyperactivity-in-primary-rat-neural-cells
#17
Yuji Kaneko, Colleen Pappas, Teresita Malapira, Fernando Ĺ Vale, Naoki Tajiri, Cesar V Borlongan
BACKGROUND/AIMS: Neuroinflammatory processes have been implicated in the pathophysiology of seizure/epilepsy. High mobility group box 1 (HMGB1), a non-histone DNA binding protein, behaves like an inflammatory cytokine in response to epileptogenic insults. Kainic acid (KA) is an excitotoxic reagent commonly used to induce epilepsy in rodents. However, the molecular mechanism by which KA-induced HMGB1 affords the initiation of epilepsy, especially the role of extracellular HMGB1 in neurotransmitter expression, remains to be elucidated...
February 20, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28222245/translation-rewiring-at-the-heart-of-phenotype-switching-in-melanoma
#18
Eleonora Leucci, Pierre Close, Jean-Christophe Marine
During tumor progression cancer cells are constantly challenged by intrinsic oncogene-induced and extrinsic micro-environmental stress signals such as hypoxia, nutrient deprivation, oxidative and genotoxic stress. Under these suboptimal growth conditions cancer cells activate an Integrative Stress Response (ISR), which results in a transient decrease in energy consumption followed by a cellular adaptation phase and possibly recovery, if the environmental conditions become more favorable. Translation is a very high energy-consuming process; it is therefore not surprising that to minimize energy consumption cancer cells turn down global protein synthesis rates while reprograming translation towards specific transcripts required for survival and adaptation...
February 21, 2017: Pigment Cell & Melanoma Research
https://www.readbyqxmd.com/read/28222000/fast-prediction-of-protein-methylation-sites-using-a-sequence-based-feature-selection-technique
#19
Leyi Wei, Pengwei Xing, Gaotao Shi, Zhi-Liang Ji, Quan Zou
Protein methylation, an important post-translational modification, plays crucial roles in many cellular processes. The accurate prediction of protein methylation sites is fundamentally important for revealing the molecular mechanisms undergoing methylation. In recent years, computational prediction based on machine learning algorithms has emerged as a powerful and robust approach for identifying methylation sites, and much progress has been made in predictive performance improvement. However, the predictive performance of existing methods is not satisfactory in terms of overall accuracy...
February 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28221990/an-integrated-circuit-for-simultaneous-extracellular-electrophysiology-recording-and-optogenetic-neural-manipulation
#20
Chang Hao Chen, Elizabeth A McCullagh, Sio Hang Pun, Peng Un Mak, Mang I Vai, Pui In Mak, Achim Klug, Tim C Lei
OBJECTIVE: The ability to record and to control action potential firing in neuronal circuits is critical to understand how the brain functions. The objective of this study is to develop a monolithic integrated circuit (IC) to record action potentials and simultaneously control action potential firing using optogenetics. METHODS: A low-noise and high input impedance (or low input capacitance) neural recording amplifier is combined with a high current laser/light-emitting diode (LED) driver in a single IC...
March 2017: IEEE Transactions on Bio-medical Engineering
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