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Results for “modularity”

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At least 811 records · Page 45Linked to original sources
PubMed2003

BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3.

Programmed destruction of regulatory proteins through the ubiquitin-proteasome system is a widely used mechanism for controlling signalling pathways. Cullins are proteins that function as scaffolds for modular ubiquitin ligases typified by the SCF (Skp1-Cul1-F-box) complex. The substrate selectivity of these E3 ligases is dictated by a specificity module that binds cullins. In the SCF complex, this module is composed of Skp1, which binds directly to Cul1, and a member of the F-box family of proteins. F-box proteins bind Skp1 through the F-box motif, and substrates by means of carboxy-terminal protein interaction domains. Similarly, Cul2 and Cul5 interact with BC-box-containing specificity factors through the Skp1-like protein elongin C. Cul3 is required for embryonic development in mammals and Caenorhabditis elegans but its specificity module is unknown. Here we report the identification of a large family of BTB-domain proteins as substrate-specific adaptors for C. elegans CUL-3. Biochemical studies using the BTB protein MEL-26 and its genetic target MEI-1 (refs 12, 13) indicate that BTB proteins merge the functional properties of Skp1 and F-box proteins into a single polypeptide.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Evidence for dynamically organized modularity in the yeast protein-protein interaction network.

In apparently scale-free protein-protein interaction networks, or 'interactome' networks, most proteins interact with few partners, whereas a small but significant proportion of proteins, the 'hubs', interact with many partners. Both biological and non-biological scale-free networks are particularly resistant to random node removal but are extremely sensitive to the targeted removal of hubs. A link between the potential scale-free topology of interactome networks and genetic robustness seems to exist, because knockouts of yeast genes encoding hubs are approximately threefold more likely to confer lethality than those of non-hubs. Here we investigate how hubs might contribute to robustness and other cellular properties for protein-protein interactions dynamically regulated both in time and in space. We uncovered two types of hub: 'party' hubs, which interact with most of their partners simultaneously, and 'date' hubs, which bind their different partners at different times or locations. Both in silico studies of network connectivity and genetic interactions described in vivo support a model of organized modularity in which date hubs organize the proteome, connecting biological processes--or modules--to each other, whereas party hubs function inside modules.

Computer Simulation↗
PubMed2006

Proteome survey reveals modularity of the yeast cell machinery.

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation. The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.

Genome, Fungal↗
PubMed2004

Modular epistasis in yeast metabolism.

Epistatic interactions, manifested in the effects of mutations on the phenotypes caused by other mutations, may help uncover the functional organization of complex biological networks. Here, we studied system-level epistatic interactions by computing growth phenotypes of all single and double knockouts of 890 metabolic genes in Saccharomyces cerevisiae, using the framework of flux balance analysis. A new scale for epistasis identified a distinctive trimodal distribution of these epistatic effects, allowing gene pairs to be classified as buffering, aggravating or noninteracting. We found that the ensuing epistatic interaction network could be organized hierarchically into function-enriched modules that interact with each other 'monochromatically' (i.e., with purely aggravating or purely buffering epistatic links). This property extends the concept of epistasis from single genes to functional units and provides a new definition of biological modularity, which emphasizes interactions between, rather than within, functional modules. Our approach can be used to infer functional gene modules from purely phenotypic epistasis measurements.

Algorithms↗
PubMed2005

Modularity and evolutionary constraint on proteins.

Modularity, which has been found in the functional and physical protein interaction networks of many organisms, has been postulated to affect both the mode and tempo of evolution. Here I show that in the yeast Saccharomyces cerevisiae, protein interaction hubs situated in single modules are highly constrained, whereas those connecting different modules are more plastic. This pattern of change could reflect a tendency for evolutionary innovations to occur by altering the proteins and interactions between rather than within modules, in a manner somewhat similar to the evolution of new proteins through the shuffling of conserved protein domains.

Computer Simulation↗
PubMed2005

A modular and supramolecular approach to bioactive scaffolds for tissue engineering.

Bioactive polymeric scaffolds are a prerequisite for the ultimate formation of functional tissues. Here, we show that supramolecular polymers based on quadruple hydrogen bonding ureido-pyrimidinone (UPy) moieties are eminently suitable for producing such bioactive materials owing to their low-temperature processability, favourable degradation and biocompatible behaviour. Particularly, the reversible nature of the hydrogen bonds allows for a modular approach to gaining control over cellular behaviour and activity both in vitro and in vivo. Bioactive materials are obtained by simply mixing UPy-functionalized polymers with UPy-modified biomolecules. Low-molecular-weight bis-UPy-oligocaprolactones with cell adhesion promoting UPy-Gly-Arg-Gly-Asp-Ser (UPy-GRGDS) and the synergistic UPy-Pro-His-Ser-Arg-Asn (UPy-PHSRN) peptide sequences are synthesized and studied. The in vitro results indicate strong and specific cell binding of fibroblasts to the UPy-functionalized bioactive materials containing both UPy-peptides. An even more striking effect is seen in vivo where the formation of single giant cells at the interface between bioactive material and tissue is triggered.

3T3 Cells↗
PubMed2003

Modularity of music processing.

The music faculty is not a monolithic entity that a person either has or does not. Rather, it comprises a set of neurally isolable processing components, each having the potential to be specialized for music. Here we propose a functional architecture for music processing that captures the typical properties of modular organization. The model rests essentially on the analysis of music-related deficits in neurologically impaired individuals, but provides useful guidelines for exploring the music faculty in normal people, using methods such as neuroimaging.

Auditory Perception↗
PubMed2004

Modular phakoemulsification training adapted for a left-handed trainee.

BACKGROUND: The increasing demand for high-volume, high-quality cataract surgery creates additional challenges for surgeons providing phakoemulsification training. We describe the modular training programme used by the Worcester Eye Department for inexperienced trainees and the adaptation of this programme to the needs of a left-handed trainee. METHODS: The intraoperative complications of a left-handed trainees' first 161 cases are reported. RESULTS: In this series, there was one case of vitreous loss (0.62%) and one case of posterior capsular tear (0.62%). Two cases developed stable anterior capsular tears (1.24%) and two cases required a single suture to ensure wound stability. CONCLUSION: We demonstrate a safe, effective and flexible method of phakoemulsification training.

Clinical Competence↗
PubMed2003

Stereoselective degradation of aqueous endosulfan in modular estuarine mesocosms: formation of endosulfan gamma-hydroxycarboxylate.

Solutions of alpha-endosulfan, beta-endosulfan, and technical grade endosulfan (70alpha:30beta) were added to modular estuarine mesocosms; the kinetics and degradation products from each mesocosm are reported. The persistent product endosulfan sulfate was generated in all cases; however, its yield was approximately a factor of three higher from alpha-endosulfan relative to beta-endosulfan. Beta-endosulfan hydrolyzed faster than alpha-endosulfan to endosulfan diol, which then rapidly degraded to endosulfan ether, endosulfan alpha-hydroxyether (major product), and endosulfan lactone. The ring-opened form of the lactone, endosulfan gamma-hydroxycarboxylate, is reported for the first time; it appears to be a terminal product, at least over the timescale of the experiment. The equilibrium between endosulfan gamma-hydroxycarboxylate and endosulfan lactone is dependent on pH, as only the protonated form of the gamma-hydroxy acid undergoes ring-closure. The pKa of the gamma-hydroxy acid was determined to be 5.7, implying that the lactone will quickly open and deprontonate under environmentally relevant conditions.

Biological Availability↗
PubMed2003

Bifurcated, modular syntheses of chiral annulet triazacyclononanes.

Three chiral 2,6-disubstituted tri-N-methyl azamacrocycles have been prepared by modular methods. These macrocycles were accessed from three chiral 1,4,7-triazaheptanes intermediates that were prepared by two independent routes. The first of these routes involved the benzylamine opening of chiral tosyl aziridines followed by debenzylation but was problematic on solubility grounds. A second, more effective, route was developed which avoided debenzylation by using ammonia in the nucleophilic opening of chiral tosyl aziridines.

Aza Compounds↗
PubMed2004

Loss of co-linearity by modular polyketide synthases: a mechanism for the evolution of chemical diversity.

Modular polyketide synthases biosynthesise natural products through successive Claisen-type condensations, where one module is responsible for one round of chain extension. This review describes recent findings where this rule of co-linearity is broken, either by one module being bypassed (skipping) or through one module being used for multiple chain extension events (stuttering).

Biological Evolution↗
PubMed2004

Polysiloxane-bound ligand accelerated catalysis: a modular approach to heterogeneous and homogeneous macromolecular asymmetric dihydroxylation ligands.

Polysiloxane acts as a modular scaffold for macromolecular reagent development. Two separate components were covalently integrated into one material, one constituent provided reagent functionality, the other modulated solubility. In particular cinchona alkaloid based ligands used in the osmium tetroxide catalyzed asymmetric dihydroxylation (AD) reaction were covalently attached to commercially available polysiloxane. To enhance the reactivity of these polymeric ligands, multifunctional reagents were designed to include both the cinchona alkaloid and an alkoxyethylester solubilizing moiety providing random co-polymers. While the mono-functional materials led to heterogeneous conditions, the bi-functional polymers resulted in homogeneous reaction mixtures. Although both reagent types provided diol products with excellent yield and selectivity (>99% ee in nearly quantitative yield) the homogeneous analog has nearly twice the reactivity. Every repeat unit in the heterogeneous material was functionalized along the polysiloxane backbone while approximately half of these sites contained ligand in the homogeneous version. This approach led to macromolecular catalysts with high loadings of ligand and therefore materials with very low equivalent weights. Although these polymers are highly loaded they do maintain reactivity on a par with their free ligand counterpart. Using straightforward purification techniques (i.e. precipitation, simple filtration, or ultrafiltration) these polymeric ligands were easily separated from diol product and reused multiple times. Polysiloxane is a viable support for the catalysis of AD reactions and may provide a generally useful backbone for other catalytic systems.

Alkaloids↗
PubMed2004

A modular ditopic crown-shielded phosphate ion-pair receptor.

The synthesis of a modular hybrid receptor containing both an aza macrocycle and crown ether is described; a complete thermodynamic characterisation of the binding properties, in water, of the zinc(II) complex of the receptor towards phosphate is presented and the parameters are compared to those of the aza macrocycle precursor.

Journal Article↗
PubMed2005

Synthesis of the non-classical acetogenin mucocin: a modular approach based on olefinic coupling reactions.

A three component modular synthesis of the potent antitumor agent mucocin, based on olefinic coupling reactions, is described. A cross-metathesis on tetrahydropyran and tetrahydrofuran alkene components was used to assemble a stereochemically complex, non-adjacently-linked bicyclic ether. The latter was elaborated to a sulfone and partnered with a butenolide aldehyde component in a Julia-Kocienski olefination to provide the mucocin framework, which was converted to the natural product after hydrogenation and alcohol deprotection.

Alkenes↗