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https://www.readbyqxmd.com/read/28225828/systematic-analysis-of-non-structural-protein-features-for-the-prediction-of-ptm-function-potential-by-artificial-neural-networks
#1
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/28224978/methylated-antibody-affinity-purification-to-improve-proteomic-identification-of-plant-rna-polymerase-pol-v-complex-and-the-interacting-proteins
#2
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
#3
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/28223095/palmitoylation-of-plasmodium-alveolins-promotes-cytoskeletal-function
#4
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/28223047/diversity-in-sequences-post-translational-modifications-and-expected-pharmacological-activities-of-toxins-from-four-conus-species-revealed-by-the-combination-of-cutting-edge-proteomics-transcriptomics-and-bioinformatics
#5
Michel Degueldre, Marion Verdenaud, Garikoitz Legarda, Rebeca Minambres, Sheila Zuniga, Mathieu Leblanc, Nicolas Gilles, Frederic Ducancel, Edwin De Pauw, Loic Quinton
Venomous animals have developed a huge arsenal of reticulated peptides for defense and predation. Based on various scaffolds, they represent a colossal pharmacological diversity, making them top candidates for the development of innovative drugs. Instead of relying on the classical, low-throughput bioassay-guided approach to identify innovative bioactive peptides, this work exploits a recent paradigm to access to venom diversity. This strategy bypasses the classical approach by combining high-throughput transcriptomics, proteomics and bioinformatics cutting-edge technologies to generate reliable peptide sequences...
February 18, 2017: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/28222786/post-translational-modification-of-parkin
#6
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/28222432/extracellular-hmgb1-modulates-glutamate-metabolism-associated-with-kainic-acid-induced-epilepsy-like-hyperactivity-in-primary-rat-neural-cells
#7
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/28222000/fast-prediction-of-protein-methylation-sites-using-a-sequence-based-feature-selection-technique
#8
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/28220131/plant-stress-responses-and-phenotypic-plasticity-in-the-epigenomics-era-perspectives-on-the-grapevine-scenario-a-model-for-perennial-crop-plants
#9
Ana M Fortes, Philippe Gallusci
Epigenetic marks include Histone Post-Translational Modifications and DNA methylation which are known to participate in the programming of gene expression in plants and animals. These epigenetic marks may be subjected to dynamic changes in response to endogenous and/or external stimuli and can have an impact on phenotypic plasticity. Studying how plant genomes can be epigenetically shaped under stressed conditions has become an essential issue in order to better understand the molecular mechanisms underlying plant stress responses and enabling epigenetic in addition to genetic factors to be considered when breeding crop plants...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28218850/impact-of-phosphorylation-and-pseudo-phosphorylation-on-the-early-stages-of-aggregation-of-the-microtubule-associated-protein-tau
#10
Dmitriy V Prokopovich, John W Whittaker, Micaiah M Muthee, Azka Ahmed, Luca Larini
The microtubule associated protein tau regulates the stability of microtubules within neurons in the central nervous system. In turn, microtubules are responsible for the remodeling of the cytoskeleton that ultimately leads to the formation or pruning of new connections among neurons. As a consequence, dysfunction of tau is associated with many forms of dementia as well as Alzheimer's disease. In the brain, tau activity is regulated by its phosphorylation state. Phosphorylation is a post-translational modification of proteins that adds a phosphate group to the side chain of an amino acid...
February 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28218637/mechanisms-of-chromosome-congression-during-mitosis
#11
REVIEW
Helder Maiato, Ana Margarida Gomes, Filipe Sousa, Marin Barisic
Chromosome congression during prometaphase culminates with the establishment of a metaphase plate, a hallmark of mitosis in metazoans. Classical views resulting from more than 100 years of research on this topic have attempted to explain chromosome congression based on the balance between opposing pulling and/or pushing forces that reach an equilibrium near the spindle equator. However, in mammalian cells, chromosome bi-orientation and force balance at kinetochores are not required for chromosome congression, whereas the mechanisms of chromosome congression are not necessarily involved in the maintenance of chromosome alignment after congression...
February 17, 2017: Biology
https://www.readbyqxmd.com/read/28215712/palmitoylation-of-cysteine-415-of-cb1-receptor-affects-ligand-stimulated-internalization-and-selective-interaction-with-membrane-cholesterol-and-caveolin-1
#12
Sergio Oddi, Tomasz Maciej Stepniewski, Antonio Totaro, Jana Selent, Lucia Scipioni, Beatrice Dufrusine, Filomena Fezza, Enrico Dainese, Mauro Maccarrone
We previously demonstrated that CB1 receptor is palmitoylated at cysteine 415, and that such a post-translational modification affects its biological activity. To assess the molecular mechanisms responsible for modulation of CB1 receptor function by S-palmitoylation, in this study biochemical and morphological approaches were paralleled with computational analyses. Molecular dynamics simulations suggested that this acyl chain stabilizes helix 8 as well as the interaction of CB1 receptor with membrane cholesterol...
February 12, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28213314/emerging-themes-of-regulation-at-the-golgi
#13
REVIEW
Stefanie L Makowski, Thuy Tt Tran, Seth J Field
The Golgi is generally recognized for its central role in the secretory pathway to orchestrate protein post-translational modification and trafficking of proteins and lipids to their final destination. Despite the common view of the Golgi as an inert sorting organelle, emerging data demonstrate that important signaling events occur at the Golgi, including those that regulate the trafficking function of the Golgi. The phosphatidylinositol-4-phosphate/GOLPH3/MYO18A/F-actin complex serves as a hub for signals that regulate Golgi trafficking function...
February 14, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28212948/the-importance-of-the-glycosylation-of-antimicrobial-peptides-natural-and-synthetic-approaches
#14
REVIEW
Natalia G Bednarska, Brendan W Wren, Sam J Willcocks
Glycosylation is one of the most prevalent post-translational modifications of a protein, with a defining impact on its structure and function. Many of the proteins involved in the innate or adaptive immune response, including cytokines, chemokines, and antimicrobial peptides (AMPs), are glycosylated, contributing to their myriad activities. The current availability of synthetic coupling and glycoengineering technology makes it possible to customise the most beneficial glycan modifications for improved AMP stability, microbicidal potency, pathogen specificity, tissue or cell targeting, and immunomodulation...
February 14, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28212627/genome-wide-identification-of-direct-hbx-genomic-targets
#15
Francesca Guerrieri, Laura Belloni, Daniel D'Andrea, Natalia Pediconi, Loredana Le Pera, Barbara Testoni, Cecilia Scisciani, Oceane Floriot, Fabien Zoulim, Anna Tramontano, Massimo Levrero
BACKGROUND: The Hepatitis B Virus (HBV) HBx regulatory protein is required for HBV replication and involved in HBV-related carcinogenesis. HBx interacts with chromatin modifying enzymes and transcription factors to modulate histone post-translational modifications and to regulate viral cccDNA transcription and cellular gene expression. Aiming to identify genes and non-coding RNAs (ncRNAs) directly targeted by HBx, we performed a chromatin immunoprecipitation sequencing (ChIP-Seq) to analyse HBV recruitment on host cell chromatin in cells replicating HBV...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212602/happi-2-a-comprehensive-and-high-quality-map-of-human-annotated-and-predicted-protein-interactions
#16
Jake Y Chen, Ragini Pandey, Thanh M Nguyen
BACKGROUND: Human protein-protein interaction (PPI) data is essential to network and systems biology studies. PPI data can help biochemists hypothesize how proteins form complexes by binding to each other, how extracellular signals propagate through post-translational modification of de-activated signaling molecules, and how chemical reactions are coupled by enzymes involved in a complex biological process. Our capability to develop good public database resources for human PPI data has a direct impact on the quality of future research on genome biology and medicine...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212427/rbm46-regulates-mouse-embryonic-stem-cell-differentiation-by-targeting-%C3%AE-catenin-mrna-for-degradation
#17
Lei Zhai, Chenchen Wang, Yuanfan Chen, Shixin Zhou, Lingsong Li
Embryonic stem cells (ESCs) are pluripotent cells and have the capability for differentiation into any of the three embryonic germ layers. The Wnt/β-Catenin pathway has been shown to play an essential role in ESC differentiation regulation. Activation of β-Catenin by post-translational modification has been extensively studied. However, mechanism(s) of post-transcriptional regulation of β-Catenin are not well defined. In this study, we report an RNA recognition motif-containing protein (RNA binding motif protein 46, RBM46) which regulates the degradation of β-Catenin mRNA...
2017: PloS One
https://www.readbyqxmd.com/read/28211924/a-selfish-b-chromosome-induces-genome-elimination-by-disrupting-the-histone-code-in-the-jewel-wasp-nasonia-vitripennis
#18
John C Aldrich, Alexandra Leibholz, Manjinder S Cheema, Juan Ausiό, Patrick M Ferree
Intragenomic conflict describes a phenomenon in which genetic elements act 'selfishly' to gain a transmission advantage at the expense of the whole genome. A non-essential, selfish B chromosome known as Paternal Sex Ratio (PSR) induces complete elimination of the sperm-derived hereditary material in the jewel wasp Nasonia vitripennis. PSR prevents the paternal chromatin from forming chromosomes during the first embryonic mitosis, leading to its loss. Although paternally transmitted, PSR evades self-elimination in order to be inherited...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211672/proteomic-analysis-of-post-synaptic-protein-complexes-underlying-neuronal-plasticity
#19
Anthony J Baucum
Normal neuronal communication and synaptic plasticity at glutamatergic synapses requires dynamic regulation of postsynaptic molecules. Protein expression and protein post-translational modifications regulate protein interactions that underlie this organization. In this review, we highlight data obtained over the last 20 years that have used qualitative and quantitative proteomics-based approaches to identify postsynaptic protein complexes. Herein, we describe how these proteomics studies have helped lay the foundation for understanding synaptic physiology and perturbations in synaptic signaling observed in different pathologies...
February 17, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28210246/prospects-of-in-vivo-incorporation-of-non-canonical-amino-acids-for-the-chemical-diversification-of-antimicrobial-peptides
#20
Tobias Baumann, Jessica H Nickling, Maike Bartholomae, Andrius Buivydas, Oscar P Kuipers, Nediljko Budisa
The incorporation of non-canonical amino acids (ncAA) is an elegant way for the chemical diversification of recombinantly produced antimicrobial peptides (AMPs). Residue- and site-specific installation methods in several bacterial production hosts hold great promise for the generation of new-to-nature AMPs, and can contribute to tackle the ongoing emergence of antibiotic resistance in pathogens. Especially from a pharmacological point of view, desirable improvements span pH and protease resistance, solubility, oral availability and circulation half-life...
2017: Frontiers in Microbiology
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