hPP Corpus: A Tagged Biomedical Corpus for Automatic  Extraction of Human Protein Phosphorylation for Understanding  Cellular Functions

In the present work, we compared the outcome of hyperosmotic and isosmotic shrinkage on ion transport and protein phosphorylation in C11-MDCK cells resembling intercalated cells from collecting ducts and in vascular smooth muscle cells (VSMC) from the rat aorta. Hyperosmotic shrinkage was triggered by cell exposure to hypertonic medium, whereas isosmotic shrinkage was evoked by cell transfer from an hypoosmotic to an isosmotic environment. Despite a similar cell volume decrease of 40%–50%, the consequences of hyperosmotic and isosmotic shrinkage on cellular functions were sharply different. In C11-MDCK and VSMC, hyperosmotic shrinkage completely inhibited Na+,K+-ATPase and Na+,Pi cotransport. In contrast, in both types of cells isosmotic shrinkage slightly increased rather than suppressed Na+,K+-ATPase and did not change Na+,Pi cotransport. In C11-MDCK cells, phosphorylation of JNK1/2 and Erk1/2 mitogen-activated protein kinases was augmented in hyperosmotically shrunken cells by ∼7- and 2-fold, respectively, but was not affected in cells subjected to isosmotic shrinkage. These results demonstrate that the data obtained in cells subjected to hyperosmotic shrinkage cannot be considered as sufficient proof implicating cell volume perturbations in the regulation of cellular functions under isosmotic conditions.

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A synthesis of over 9,000 mass spectrometry experiments reveals the core set of human protein complexes

10.1101/092361 ◽

2016 ◽

Cited By ~ 1

Author(s):

Kevin Drew ◽

Chanjae Lee ◽

Ryan L. Huizar ◽

Fan Tu ◽

Blake Borgeson ◽

...

Keyword(s):

Mass Spectrometry ◽

Protein Interactions ◽

Protein Complexes ◽

Genetic Diseases ◽

Intraflagellar Transport ◽

Human Protein ◽

Disease Genes ◽

Cellular Functions ◽

The Core

AbstractMacromolecular protein complexes carry out many of the essential functions of cells, and many genetic diseases arise from disrupting the functions of such complexes. Currently there is great interest in defining the complete set of human protein complexes, but recent published maps lack comprehensive coverage. Here, through the synthesis of over 9,000 published mass spectrometry experiments, we present hu.MAP, the most comprehensive and accurate human protein complex map to date, containing >4,600 total complexes, >7,700 proteins and >56,000 unique interactions, including thousands of confident protein interactions not identified by the original publications. hu.MAP accurately recapitulates known complexes withheld from the learning procedure, which was optimized with the aid of a new quantitative metric (k-cliques) for comparing sets of sets. The vast majority of complexes in our map are significantly enriched with literature annotations and the map overall shows improved coverage of many disease-associated proteins, as we describe in detail for ciliopathies. Using hu.MAP, we predicted and experimentally validated candidate ciliopathy disease genes in vivo in a model vertebrate, discovering CCDC138, WDR90, and KIAA1328 to be new cilia basal body/centriolar satellite proteins, and identifying ANKRD55 as a novel member of the intraflagellar transport machinery. By offering significant improvements to the accuracy and coverage of human protein complexes, hu.MAP (http://proteincomplexes.org) serves as a valuable resource for better understanding the core cellular functions of human proteins and helping to determine mechanistic foundations of human disease.

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A reliable and unbiased human protein network with the disparity filter

10.1101/207761 ◽

2017 ◽

Cited By ~ 1

Author(s):

Gregorio Alanis-Lobato ◽

Miguel A. Andrade-Navarro

Keyword(s):

Experimental Evidence ◽

Protein Interactions ◽

Living Cell ◽

Human Proteome ◽

Human Protein ◽

Protein Network ◽

Small Scale ◽

Cellular Functions ◽

Wiring Diagram ◽

Human Interactome

AbstractThe living cell operates thanks to an intricate network of protein interactions. Proteins activate, transport, degrade, stabilise and participate in the production of other proteins. As a result, a reliable and systematically generated protein wiring diagram is crucial for a deeper understanding of cellular functions. Unfortunately, current human protein networks are noisy and incomplete. Also, they suffer from both study and technical biases: heavily studied proteins (e.g. those of pharmaceutical interest) are known to be involved in more interactions than proteins described in only a few publications. Here, we use the experimental evidence supporting the interaction between proteins, in conjunction with the so-called disparity filter, to construct a reliable and unbiased proteome-scale human interactome. The application of a global filter, i.e. only considering interactions with multiple pieces of evidence, would result in an excessively pruned network. In contrast, the disparity filter preserves interactions supported by a statistically significant number of studies and does not overlook small-scale protein associations. The resulting disparity-filtered protein network covers 67% of the human proteome and retains most of the network’s weight and connectivity properties.

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The complex interplay in the regulation of cardiac pathophysiologic functionalities by protein kinases and phosphatases

Journal of Cardiology and Cardiovascular Medicine ◽

10.29328/journal.jccm.1001118 ◽

2021 ◽

Vol 6 (3) ◽

pp. 048-054

Author(s):

Chukwuma Sr Chrysanthus

Keyword(s):

Heart Failure ◽

Protein Phosphorylation ◽

Cardiovascular System ◽

Protein Kinases ◽

Cell Fate ◽

Body Burden ◽

The Body ◽

Discrete Control ◽

Cellular Functions ◽

Cardiac Excitation

Protein phosphorylation regulates several dimensions of cell fate and is substantially dysregulated in pathophysiological instances as evident spatiotemporally via intracellular localizations or compartmentalizations with discrete control by specific kinases and phosphatases. Cardiovascular disease manifests as an intricately complex entity presenting as a derangement of the cardiovascular system. Cardiac or heart failure connotes the pathophysiological state in which deficient cardiac output compromises the body burden and requirements. Protein kinases regulate several pathophysiological processes and are emerging targets for drug lead or discovery. The protein kinases are family members of the serine/threonine phosphatases. Protein kinases covalently modify proteins by attaching phosphate groups from ATP to residues of serine, threonine and/or tyrosine. Protein kinases and phosphatases are pivotal in the regulatory mechanisms in the reversible phosphorylation of diverse effectors whereby discrete signaling molecules regulate cardiac excitation and contraction. Protein phosphorylation is critical for the sustenance of cardiac functionalities. The two major contributory ingredients to progressive myocardium derangement are dysregulation of Ca2+ processes and contemporaneous elevated concentrations of reactive oxygen species, ROS. Certain cardiac abnormalities include cardiac myopathy or hypertrophy due to response in untoward haemodynamic demand with concomitant progressive heart failure. The homeostasis or equilibrium between protein kinases and phosphatases influence cardiac morphology and excitability during pathological and physiological processes of the cardiovascular system. Inasmuch as protein kinases regulate numerous dimensions of normal cellular functions, the pathophysiological dysfunctionality of protein kinase signaling pathways undergirds the molecular aspects of several cardiovascular diseases or disorders as related in this study. These have presented protein kinases as essential and potential targets for drug discovery and heart disease therapy.

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Protein phosphorylation: cellular functions and therapeutic perspectives

Journal of Cancer Research and Clinical Oncology ◽

10.1007/s004320100288 ◽

2001 ◽

Vol 127 (12) ◽

pp. 744-750 ◽

Cited By ~ 2

Author(s):

F. Marks

Keyword(s):

Protein Phosphorylation ◽

Cellular Functions

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Newfound coding potential of transcripts unveils missing members of human protein communities

10.1101/2020.12.02.406710 ◽

2020 ◽

Author(s):

Sebastien Leblanc ◽

Marie A Brunet ◽

Jean-François Jacques ◽

Amina M Lekehal ◽

Andréa Duclos ◽

...

Keyword(s):

Interaction Network ◽

Open Reading Frames ◽

Human Protein ◽

Cellular Functions ◽

Reading Frame ◽

Functional Roles ◽

Protein Protein Interaction ◽

Coding Regions ◽

Alternative Protein ◽

Genes Encoding

AbstractRecent proteogenomic approaches have led to the discovery that regions of the transcriptome previously annotated as non-coding regions (i.e. UTRs, open reading frames overlapping annotated coding sequences in a different reading frame, and non-coding RNAs) frequently encode proteins (termed alternative proteins). This suggests that previously identified protein communities are partially incomplete since alternative proteins are not present in conventional protein databases. Here we incorporate this increased diversity in the re-analysis of a high throughput human network proteomics dataset thereby revealing the presence of 203 alternative proteins within 163 distinct communities associated with a wide variety of cellular functions and pathologies. We found 19 genes encoding both an annotated (reference) and an alternative protein interacting with each other. Of the 136 alternative proteins encoded by pseudogenes, 38 are direct interactors of reference proteins encoded by their respective parental gene. Finally, we experimentally validate several interactions involving alternative proteins. These data improve the blueprints of the human protein-protein interaction network and suggest functional roles for hundreds of alternative proteins.

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Surface Structure of Nucleated Animal Cells: Carbon Replicas

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100060611 ◽

1967 ◽

Vol 25 ◽

pp. 120-121

Author(s):

Robert M. Glaeser ◽

Thea B. Scott

Keyword(s):

Cell Surface ◽

Surface Structure ◽

Particle Diameter ◽

Cellular Functions ◽

Animal Cells ◽

Replica Technique ◽

Carbon Replica ◽

Characteristic Particle ◽

Cell Surface Structure ◽

Carbon Replicas

The carbon-replica technique can be used to obtain information about cell-surface structure that cannot ordinarily be obtained by thin-section techniques. Mammalian erythrocytes have been studied by the replica technique and they appear to be characterized by a pebbly or “plaqued“ surface texture. The characteristic “particle” diameter is about 200 Å to 400 Å. We have now extended our observations on cell-surface structure to chicken and frog erythrocytes, which possess a broad range of cellular functions, and to normal rat lymphocytes and mouse ascites tumor cells, which are capable of cell division. In these experiments fresh cells were washed in Eagle's Minimum Essential Medium Salt Solution (for suspension cultures) and one volume of a 10% cell suspension was added to one volume of 2% OsO4 or 5% gluteraldehyde in 0.067 M phosphate buffer, pH 7.3. Carbon replicas were obtained by a technique similar to that employed by Glaeser et al. Figure 1 shows an electron micrograph of a carbon replica made from a chicken erythrocyte, and Figure 2 shows an enlarged portion of the same cell.

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Multimode light microscopy and fluorescence-based reagents as tools for the study of chemical and molecular dynamics of living cells and tissues

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100122496 ◽

1992 ◽

Vol 50 (1) ◽

pp. 418-419

Author(s):

D. L. Taylor

Keyword(s):

Living Cells ◽

Cellular Level ◽

Molecular Techniques ◽

Cellular Functions ◽

Macromolecular Assemblies ◽

Cell Functions ◽

Molecular Events ◽

Yield Information ◽

Full Knowledge ◽

Structural Methods

Cells function through the complex temporal and spatial interplay of ions, metabolites, macromolecules and macromolecular assemblies. Biochemical approaches allow the investigator to define the components and the solution chemical reactions that might be involved in cellular functions. Static structural methods can yield information concerning the 2- and 3-D organization of known and unknown cellular constituents. Genetic and molecular techniques are powerful approaches that can alter specific functions through the manipulation of gene products and thus identify necessary components and sequences of molecular events. However, full knowledge of the mechanism of particular cell functions will require direct measurement of the interplay of cellular constituents. Therefore, there has been a need to develop methods that can yield chemical and molecular information in time and space in living cells, while allowing the integration of information from biochemical, molecular and genetic approaches at the cellular level.

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Correlation Between Cellular Functions and Morphological Changes of Human Trophoblast in Vitro

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100116620 ◽

1975 ◽

Vol 33 ◽

pp. 600-601

Author(s):

John C. Garancis ◽

Robert O. Hussa ◽

Michael T. Story ◽

Donald Yorde ◽

Roland A. Pattillo

Keyword(s):

Electron Microscopy ◽

Cellular Proliferation ◽

Morphological Changes ◽

Culture Fluid ◽

Cellular Functions ◽

Human Trophoblast ◽

Transmission Electron ◽

Marked Activity ◽

Malignant Trophoblast

Human malignant trophoblast cells in continuous culture were incubated for 3 days in medium containing 1 mM N6-O2'-dibutyryl cyclic adenosine 3':5'-monophosphate (dibutyryl cyclic AMP) and 1 mM theophylline. The culture fluid was replenished daily. Stimulated cultures secreted many times more chorionic gonadotropin and estrogens than did control cultures in the absence of increased cellular proliferation. Scanning electron microscopy revealed remarkable surface changes of stimulated cells. Control cells (not stimulated) were smooth or provided with varying numbers of microvilli (Fig. 1). The latter, usually, were short and thin. The surface features of stimulated cells were considerably different. There was marked increase of microvilli which appeared elongated and thick. Many cells were covered with confluent polypoid projections (Fig. 2). Transmission electron microscopy demonstrated marked activity of cytoplasmic organelles. Mitochondria were increased in number and size; some giant forms with numerous cristae were observed.

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Signal-regulated oxidation of proteins via MICAL

Biochemical Society Transactions ◽

10.1042/bst20190866 ◽

2020 ◽

Vol 48 (2) ◽

pp. 613-620

Author(s):

Clara Ortegón Salas ◽

Katharina Schneider ◽

Christopher Horst Lillig ◽

Manuela Gellert

Keyword(s):

Signal Transduction ◽

Hydrogen Peroxide ◽

Cell Death ◽

Redox Regulation ◽

Signal Transduction Pathways ◽

Cellular Functions ◽

Intracellular Signals ◽

Amino Acid Side Chains ◽

Specific Receptors ◽

Sulfur Containing

Processing of and responding to various signals is an essential cellular function that influences survival, homeostasis, development, and cell death. Extra- or intracellular signals are perceived via specific receptors and transduced in a particular signalling pathway that results in a precise response. Reversible post-translational redox modifications of cysteinyl and methionyl residues have been characterised in countless signal transduction pathways. Due to the low reactivity of most sulfur-containing amino acid side chains with hydrogen peroxide, for instance, and also to ensure specificity, redox signalling requires catalysis, just like phosphorylation signalling requires kinases and phosphatases. While reducing enzymes of both cysteinyl- and methionyl-derivates have been characterised in great detail before, the discovery and characterisation of MICAL proteins evinced the first examples of specific oxidases in signal transduction. This article provides an overview of the functions of MICAL proteins in the redox regulation of cellular functions.

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