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Focus on Protein Research,
2004]
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J Protein Chem,
1997]
Our efforts to classify the functional units of many proteins, the modules, are reviewed. The data from the sequencing projects for various model organisms are extremely helpful in deducing the evolution of proteins and modules. For example, a dramatic increase of modular proteins can be observed from yeast to C. elegans in accordance with new protein functions that had to be introduced in multicellular organisms. Our sequence characterization of modules relies on sensitive similarity search algorithms and the collection of multiple sequence alignments for each module. To trace the evolution of modules and to further automate the classification, we have developed a sequence and a module alerting system that checks newly arriving sequence data for the presence of already classified modules. Using these systems, we were able to identify an unexpected similarity between extracellular C1Q modules with bacterial proteins.
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Genes Dev,
1999]
A wide variety of extracellular stimuli induce signal transduction through receptors coupled to heterotrimeric G proteins, which consist of alpha, beta, and gamma subunits (Gilman 1987). The G alpha subunit has guanine nucleotide binding and GTP hydrolysis activities. Based on function and amino acid sequence homology, the Galpha, G alph i/o, G alpha q, and G alpha 12 (Simon et al. 1991; Hepler and Gilman 1992). As exemplified by the responsiveness of our five senses to environmental stimuli, signaling mediated by trimeric G proteins is often extremely rapid and transient. A key step in achieving such a raid response is the ability of the G alpha subunit to switch between it GDP- and GTP-bound forms. The nucleotide binding state of G alpha is regulated at both the GDP dissociation and GTP hydrolysis steps. Stimulation of receptors by agonists leads to a conformational change in the receptors which can function as a guanine nucleotide exchange factor to stimulate a rapid dissociation of GDP from the inactive G alpha. The nucleotide-free G alpha is then available to bind GTP, leading to the dissociation of G alpha from the G beta gamma heterodimer. Both the G alpha and G beat gamma subunits can interact with and regulate downstream effectors that include adenylyl cyclase, phospholipase C, and ion channels (Gilman 1987; Birnbaumer 1992).
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Methods Cell Biol,
1995]
The ultimate goal of subcellular fractionation and biochemical purification is to better understand the relationships between structure and function of proteins and protein assemblies. Examples of such relationships with respect to specific gene products include the formation of stable complexes, elucidation of catalytic activities, and subcellular localization of the organellar and supramolecular levels. The detailed aspects of such relationships are not always readily predictable from genetic or molecular studies of the gene products or from their cellular localization by immunological methods. Subcellular fractionation and biochemical purification are generally prerequisites to experimental analysis of biochemical mechanisms underlying a biological phenomenon. These approaches can mutually enhance and interact with parallel cellular, genetic, and molecular analyses. To achieve such goals, methods for isolating proteins and protein assemblies must preserve both structural integrity and biological activity. Ideally, both objectives should be met; practically, it may be critical to know which of these conditions is true. In general, specific protocols must be designed for the optimal isolation, purification, and characterization of each specific protein of interest. Additionally, one wishes to achieve as high a yield as possible; however, each step in protein purification generally produces some reduction in yield...
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Cell Cycle,
2012]
Dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs) constitute an evolutionarily conserved family of protein kinases with key roles in the control of cell proliferation and differentiation. Members of the DYRK family phosphorylate many substrates, including critical regulators of the cell cycle. A recent report revealed that human DYRK2 acts as a negative regulator of G1/S transition by phosphorylating c-Jun and c-Myc, thereby inducing ubiquitination-mediated degradation. Other DYRKs also function as cell cycle regulators by modulating the turnover of their target proteins. DYRK1B can induce reversible cell arrest in a quiescent G0 state by targeting cyclin D1 for proteasomal degradation and stabilizing
p27 (Kip1). The DYRK2 ortholog of C. elegans, MBK-2, triggers the proteasomal destruction of oocyte proteins after meiosis to allow the mitotic divisions in embryo development. This review summarizes the accumulating results that provide evidence for a general role of DYRKs in the regulation of protein stability.
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WormBook,
2005]
Protein kinases are one of the largest and most influential of gene families: constituting some 2% of the proteome, they regulate almost all biochemical pathways and may phosphorylate up to 30% of the proteome. Bioinformatics and comparative genomics were used to determine the C. elegans kinome and put it in evolutionary and functional context. Kinases are deeply conserved in evolution, and the worm has family homologs for over 80% of the human kinome. Almost half of the 438 worm kinases are members of worm-specific or worm-expanded families. Such radiations include genes involved in spermatogenesis, chemosensation, Wnt signaling and FGF receptor-like kinases. The C. briggsae kinome is largely similar apart from the expanded classes, showing that such expansions are evolutionarily recent.
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Genome Biol,
2011]
Cullin proteins are molecular scaffolds that have crucial roles in the post-translational modification of cellular proteins involving ubiquitin. The mammalian cullin protein family comprises eight members (CUL1 to CUL7 and PARC), which are characterized by a cullin homology domain. CUL1 to CUL7 assemble multi-subunit Cullin-RING E3 ubiquitin ligase (CRL) complexes, the largest family of E3 ligases with more than 200 members. Although CUL7 and PARC are present only in chordates, other members of the cullin protein family are found in Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and yeast. A cullin protein tethers both a substrate-targeting unit, often through an adaptor protein, and the RING finger component in a CRL. The cullin-organized CRL thus positions a substrate close to the RING-bound E2 ubiquitin-conjugating enzyme, which catalyzes the transfer of ubiquitin to the substrate. In addition, conjugation of cullins with the ubiquitin-like molecule Nedd8 modulates activation of the corresponding CRL complex, probably through conformational regulation of the interactions between cullin's carboxy-terminal tail and CRL's RING subunit. Genetic studies in several model organisms have helped to unravel a multitude of physiological functions associated with cullin proteins and their respective CRLs. CRLs target numerous substrates and thus have an impact on a range of biological processes, including cell growth, development, signal transduction, transcriptional control, genomic integrity and tumor suppression. Moreover, mutations in CUL7 and CUL4B genes have been linked to hereditary human diseases.
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Science,
1996]
As anyone who has ever slept with a snorer, studied in a college dormitory, or lived next door to a pianist knows, tuning out one's surroundings can be a sanity-preserving skill. This ability isn't just limited to humans. Even the simplest cells can mute their own internal communication lines to tune out the racket of chemical noise made by hormones, neurotransmitters, growth factors, and other cell regulators, allowing them to damp down their responses to such stimuli after prolonged exposure. Exactly how cells achieve this "desensitization" is unclear, but in a spate of recent studies, researchers in several laboratories have closed in on one volume control for a key intracellular communication line: the "G proteins" that serve as intermediaries carrying signals from numerous hormones and neurotransmitters to the cell interior. Over the past year, the work has uncovered a large and growing family of proteins that seem to regulate the sensitivity of G protein signaling pathways in organisms ranging from yeast and nematodes to rats and even
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Calcium Binding Proteins,
2007]
Various Ca2+ binding proteins participate in many Ca2+ modulated signaling pathways as signal transducers. These Ca2+ binding proteins including Ca2+ channels, intracellular signal transducers (kinase and phosphatase), ER chaperones, and muscle components are functionally well conserved from human to nematode. C. elegans is a free-living soil nematode which has been introduced as a model organism in the early 1960s. Due to the extensive accumulation of data, it is now possible to investigate structural and functional relationships of Ca2+ binding proteins at the whole organism level. Indeed, the extensive studies in C. elegans have identified many genes encoding a variety of Ca2+ binding proteins and revealed their functions specifically involved in particular behaviors of C. elegans. In this review, we introduce C. elegans as a model animal to provide an overview of the roles of Ca2+ binding proteins on its behaviors.
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F1000Res,
2017]
The scaffold protein Par-3 ( Drosophila Bazooka) is a central organizer of cell polarity across animals. This review focuses on how the clustering of Par-3 contributes to cell polarity. It begins with the Par-3 homo-oligomerization mechanism and its regulation by Par-1 phosphorylation. The role of polarized cytoskeletal networks in distributing Par-3 clusters to one end of the cell is then discussed, as is the subsequent maintenance of polarized Par-3 clusters through hindered mobility and inhibition from the opposite pole. Finally, specific roles of Par-3 clusters are reviewed, including the bundling of microtubules, the cortical docking of centrosomes, the growth and positioning of cadherin-catenin clusters, and the inhibition of the Par-6-aPKC kinase cassette. Examples are drawn from Drosophila, Caenorhabditis elegans, mammalian cell culture, and biochemical studies.