Academic literature on the topic 'Proteolytic assemblies'
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Journal articles on the topic "Proteolytic assemblies"
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Walz, J., A. J. Koster, T. Tamura, and W. Baumeister. "Macromolecular Assemblies Designed for Controlled Proteolysis." Microscopy and Microanalysis 4, S2 (July 1998): 980–81. http://dx.doi.org/10.1017/s1431927600025022.
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Since cellular structures are rebuilt continually, protein degradation is essential for the maintenance of homeostasis. Misfolded proteins ensuing from genetic defects or environmental stress, are prone to aggregation; chaperones and proteases cooperate in minimizing such unproductive interactions. Last, but not least, protein degradation serves to terminate the lifespan of many regulatory proteins at distinct times and thus features as a key regulatory element itself. Proteins destined for degradation must be recognized and selected within the crowded environment of the cell. The stratagem of self-compartmentalization is key to controlling cellular proteolysis (1).In recent years, a number of multisubunit proteolytic complexes have been described which possess large internal cavities or nano-compartments. This allows them to confine the proteolytic action to their interior; access to these inner compartments is usually restricted to the unfolded proteins. This, in turn, makes it necessary for these proteases to interact - either in a transient or in a permanent manner
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Koppen, Mirko, Metodi D. Metodiev, Giorgio Casari, Elena I. Rugarli, and Thomas Langer. "Variable and Tissue-Specific Subunit Composition of Mitochondrial m-AAA Protease Complexes Linked to Hereditary Spastic Paraplegia." Molecular and Cellular Biology 27, no. 2 (November 13, 2006): 758–67. http://dx.doi.org/10.1128/mcb.01470-06.
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ABSTRACT The m-AAA protease, an ATP-dependent proteolytic complex in the mitochondrial inner membrane, controls protein quality and regulates ribosome assembly, thus exerting essential housekeeping functions within mitochondria. Mutations in the m-AAA protease subunit paraplegin cause axonal degeneration in hereditary spastic paraplegia (HSP), but the basis for the unexpected tissue specificity is not understood. Paraplegin assembles with homologous Afg3l2 subunits into hetero-oligomeric complexes which can substitute for yeast m-AAA proteases, demonstrating functional conservation. The function of a third paralogue, Afg3l1 expressed in mouse, is unknown. Here, we analyze the assembly of paraplegin into m-AAA complexes and monitor consequences of paraplegin deficiency in HSP fibroblasts and in a mouse model for HSP. Our findings reveal variability in the assembly of m-AAA proteases in mitochondria in different tissues. Homo-oligomeric Afg3l1 and Afg3l2 complexes and hetero-oligomeric assemblies of both proteins with paraplegin can be formed. Yeast complementation studies demonstrate the proteolytic activity of these assemblies. Paraplegin deficiency in HSP does not result in the loss of m-AAA protease activity in brain mitochondria. Rather, homo-oligomeric Afg3l2 complexes accumulate, and these complexes can substitute for housekeeping functions of paraplegin-containing m-AAA complexes. We therefore propose that the formation of m-AAA proteases with altered substrate specificities leads to axonal degeneration in HSP.
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Aweida, Dina, and Shenhav Cohen. "Breakdown of Filamentous Myofibrils by the UPS–Step by Step." Biomolecules 11, no. 1 (January 15, 2021): 110. http://dx.doi.org/10.3390/biom11010110.
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Protein degradation maintains cellular integrity by regulating virtually all biological processes, whereas impaired proteolysis perturbs protein quality control, and often leads to human disease. Two major proteolytic systems are responsible for protein breakdown in all cells: autophagy, which facilitates the loss of organelles, protein aggregates, and cell surface proteins; and the ubiquitin-proteasome system (UPS), which promotes degradation of mainly soluble proteins. Recent findings indicate that more complex protein structures, such as filamentous assemblies, which are not accessible to the catalytic core of the proteasome in vitro, can be efficiently degraded by this proteolytic machinery in systemic catabolic states in vivo. Mechanisms that loosen the filamentous structure seem to be activated first, hence increasing the accessibility of protein constituents to the UPS. In this review, we will discuss the mechanisms underlying the disassembly and loss of the intricate insoluble filamentous myofibrils, which are responsible for muscle contraction, and whose degradation by the UPS causes weakness and disability in aging and disease. Several lines of evidence indicate that myofibril breakdown occurs in a strictly ordered and controlled manner, and the function of AAA-ATPases is crucial for their disassembly and loss.
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Yang, Dongsik, Hongjian He, and Bing Xu. "Enzyme-instructed morphological transition of the supramolecular assemblies of branched peptides." Beilstein Journal of Organic Chemistry 16 (November 4, 2020): 2709–18. http://dx.doi.org/10.3762/bjoc.16.221.
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Here, we report the use of an enzymatic reaction to cleave the branch off branched peptides for inducing the morphological transition of the assemblies of the peptides. The attachment of DEDDDLLI sequences to the ε-amine of the lysine residue of a tetrapeptide produces branched peptides that form micelles. Upon the proteolytic cleavage of the branch, catalyzed by proteinase K, the micelles turn into nanofibers. We also found that the acetylation of the N-terminal of the branch increased the stability of the branched peptides. Moreover, these branched peptides facilitate the delivery of the proteins into cells. This work contributes insights for the development of peptide supramolecular assemblies via enzymatic noncovalent synthesis in cellular environment.
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Oláh, Judit, Attila Lehotzky, Tibor Szénási, and Judit Ovádi. "Anti-Aggregative Effect of the Antioxidant DJ-1 on the TPPP/p25-Derived Pathological Associations of Alpha-Synuclein." Cells 10, no. 11 (October 27, 2021): 2909. http://dx.doi.org/10.3390/cells10112909.
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DJ-1, a multi-functional protein with antioxidant properties, protects dopaminergic neurons against Parkinson’s disease (PD). The oligomerization/assembly of alpha-synuclein (SYN), promoted by Tubulin Polymerization Promoting Protein (TPPP/p25), is fatal in the early stage of PD. The pathological assembly of SYN with TPPP/p25 inhibits their proteolytic degradation. In this work, we identified DJ-1 as a new interactive partner of TPPP/p25, and revealed its influence on the association of TPPP/p25 with SYN. DJ-1 did not affect the TPPP/p25-derived tubulin polymerization; however, it did impede the toxic assembly of TPPP/p25 with SYN. The interaction of DJ-1 with TPPP/p25 was visualized in living human cells by fluorescence confocal microscopy coupled with Bifunctional Fluorescence Complementation (BiFC). While the transfected DJ-1 displayed homogeneous intracellular distribution, the TPPP/p25-DJ-1 complex was aligned along the microtubule network. The anti-aggregative effect of DJ-1 on the pathological TPPP/p25-SYN assemblies was established by the decrease in the intensity of their intracellular fluorescence (BiFC signal) and the increase in the proteolytic degradation of SYN complexed with TPPP/p25 due to the DJ-1-derived disassembly of SYN with TPPP/p25. These data obtained with HeLa and SH-SY5Y cells revealed the protective effect of DJ-1 against toxic SYN assemblies, which assigns a new function to the antioxidant sensor DJ-1.
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Uskoković, V., M.-K. Kim, W. Li, and S. Habelitz. "Enzymatic processing of amelogenin during continuous crystallization of apatite." Journal of Materials Research 23, no. 12 (December 2008): 3184–95. http://dx.doi.org/10.1557/jmr.2008.0387.
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Dental enamel forms through a protein-controlled mineralization and enzymatic degradation process with a nanoscale precision that new engineering technologies may be able to mimic. Recombinant full-length human amelogenin (rH174) and a matrix-metalloprotease (MMP-20) were used in a pH-stat titration system that enabled a continuous supply of calcium and phosphate ions over several days, mimicking the initial stages of matrix processing and crystallization in enamel in vitro. Effects on the self-assembly and crystal growth from a saturated aqueous solution containing 0.4 mg/mL rH174 and MMP-20 with the weight ratio of 1:1000 with respect to rH174 were investigated. A transition from nanospheres to fibrous amelogenin assemblies was facilitated under conditions that involved interaction between rH174 and its proteolytic cleavage products. Despite continuous titration, the levels of calcium exhibited a consistent trend of decreasing, thereby indicating a possible role in protein self-assembly. This study suggests that mimicking enamel formation in vitro requires the synergy between the aspects of matrix self-assembly, proteolysis, and crystallization.
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Yang, Jin-Kyoung, Seon-Yeong Kwak, Su-Ji Jeon, Eunjin Lee, Jong-Min Ju, Hye-In Kim, Yoon-Sik Lee, and Jong-Ho Kim. "Proteolytic disassembly of peptide-mediated graphene oxide assemblies for turn-on fluorescence sensing of proteases." Nanoscale 8, no. 24 (2016): 12272–81. http://dx.doi.org/10.1039/c6nr02815b.
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Erk, Inge, Jean-Claude Huet, Mariela Duarte, Stéphane Duquerroy, Felix Rey, Jean Cohen, and Jean Lepault. "A Zinc Ion Controls Assembly and Stability of the Major Capsid Protein of Rotavirus." Journal of Virology 77, no. 6 (March 15, 2003): 3595–601. http://dx.doi.org/10.1128/jvi.77.6.3595-3601.2003.
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ABSTRACT The recent determination of the crystal structure of VP6, the major capsid protein of rotavirus, revealed a trimer containing a central zinc ion coordinated by histidine 153 from each of the three subunits. The role of the zinc ion in the functions of VP6 was investigated by site-directed mutagenesis. The mutation of histidine 153 into a serine (H153S and H153S/S339H) did not prevent the formation of VP6 trimers. At pH <7.0, about the pK of histidine, wild-type and mutated VP6 proteins display similar properties, giving rise to identical tubular and spherical assemblies. However, at pH >7.0, histidine 153 mutant proteins did not assemble into the characteristic 45-nm-diameter tubes, in contrast to wild-type VP6. These observations showed that under conditions in which histidine residues are not charged, the properties of VP6 depended on the presence of the centrally coordinated zinc atom in the trimer. Indeed, wild-type VP6 depleted of the zinc ion by a high concentration (100 mM) of a metal-chelating agent behaved like the H153 mutant proteins. The susceptibility of wild-type VP6 to proteases is greatly increased in the absence of zinc. NH2-terminal sequencing of the proteolytic fragments showed that they all contained the β-sheet-rich VP6 head domain, which appeared to be less sensitive to protease activity than the α-helical basal domain. Finally, the mutant proteins assembled well on cores, as demonstrated by both electron microscopy and rescue of transcriptase activity. Zinc is thus not necessary for the transcription activity. All of these observations suggest that, in solution, VP6 trimers present a structural flexibility that is controlled by the presence of a zinc ion.
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Harkness, Robert W., Yuki Toyama, Zev A. Ripstein, Huaying Zhao, Alexander I. M. Sever, Qing Luan, Jacob P. Brady, Patricia L. Clark, Peter Schuck, and Lewis E. Kay. "Competing stress-dependent oligomerization pathways regulate self-assembly of the periplasmic protease-chaperone DegP." Proceedings of the National Academy of Sciences 118, no. 32 (August 6, 2021): e2109732118. http://dx.doi.org/10.1073/pnas.2109732118.
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DegP is an oligomeric protein with dual protease and chaperone activity that regulates protein homeostasis and virulence factor trafficking in the periplasm of gram-negative bacteria. A number of oligomeric architectures adopted by DegP are thought to facilitate its function. For example, DegP can form a “resting” hexamer when not engaged to substrates, mitigating undesired proteolysis of cellular proteins. When bound to substrate proteins or lipid membranes, DegP has been shown to populate a variety of cage- or bowl-like oligomeric states that have increased proteolytic activity. Though a number of DegP’s substrate-engaged structures have been robustly characterized, detailed mechanistic information underpinning its remarkable oligomeric plasticity and the corresponding interplay between these dynamics and biological function has remained elusive. Here, we have used a combination of hydrodynamics and NMR spectroscopy methodologies in combination with cryogenic electron microscopy to shed light on the apo-DegP self-assembly mechanism. We find that, in the absence of bound substrates, DegP populates an ensemble of oligomeric states, mediated by self-assembly of trimers, that are distinct from those observed in the presence of substrate. The oligomeric distribution is sensitive to solution ionic strength and temperature and is shifted toward larger oligomeric assemblies under physiological conditions. Substrate proteins may guide DegP toward canonical cage-like structures by binding to these preorganized oligomers, leading to changes in conformation. The properties of DegP self-assembly identified here suggest that apo-DegP can rapidly shift its oligomeric distribution in order to respond to a variety of biological insults.
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Tamara, Sem, Vojtech Franc, and Albert J. R. Heck. "A wealth of genotype-specific proteoforms fine-tunes hemoglobin scavenging by haptoglobin." Proceedings of the National Academy of Sciences 117, no. 27 (June 19, 2020): 15554–64. http://dx.doi.org/10.1073/pnas.2002483117.
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The serum haptoglobin protein (Hp) scavenges toxic hemoglobin (Hb) leaked into the bloodstream from erythrocytes. In humans, there are two frequently occurring allelic forms of Hp, resulting in three genotypes: Homozygous Hp 1-1 and Hp 2-2, and heterozygous Hp 2-1. The Hp genetic polymorphism has an intriguing effect on the quaternary structure of Hp. The simplest form, Hp 1-1, forms dimers consisting of two α1β units, connected by disulfide bridges. Hp 2-1 forms mixtures of linear (α1)2(α2)n-2(β)noligomers (n> 1) while Hp 2-2 occurs in cyclic (α2)n(β)noligomers (n> 2). Different Hp genotypes bind Hb with different affinities, with Hp 2-2 being the weakest binder. This behavior has a significant influence on Hp’s antioxidant capacity, with potentially distinctive personalized clinical consequences. Although Hp has been studied extensively in the past, the finest molecular details of the observed differences in interactions between Hp and Hb are not yet fully understood. Here, we determined the full proteoform profiles and proteoform assemblies of all three most common genetic Hp variants. We combined several state-of-the-art analytical methods, including various forms of chromatography, mass photometry, and different tiers of mass spectrometry, to reveal how the tens to hundreds distinct proteoforms and their assemblies influence Hp’s capacity for Hb binding. We extend the current knowledge by showing that Hb binding does not just depend on the donor’s genotype, but is also affected by variations in Hp oligomerization, glycosylation, and proteolytic processing of the Hp α-chain.
Dissertations / Theses on the topic "Proteolytic assemblies"
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Wickström, Claes. "MUC5B from the oral cavity identification of 'insoluble' assemblies and putative regulatory proteolytic events /." [Malmö] : Faculty of Odontology, Malmö University, 2002. http://catalog.hathitrust.org/api/volumes/oclc/51310732.html.
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Appolaire, Alexandre. "Etude des grands assemblages protéolytiques de la famille TET : processus d'oligomérisation et régulation fonctionnelle associée." Thesis, Grenoble, 2014. http://www.theses.fr/2014GRENV062/document.
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La protéolyse est une fonction clé de la cellule pour le maintien de l'intégrité du protéome, pour le métabolisme et pour la régulation de nombreux processus physiologiques. Le travail présenté dans cette thèse porte sur une famille de complexes peptidases cytosoliques auto-compartimentés et énergie indépendants découverts chez les Archées, les aminopeptidases TET. Chez l'Archée hyperthermophile Pyrococcus horikoshii, organisme modèle de cette étude, il existe 3 peptidases TET présentant chacune des spécificités de substrats différentes. Les caractérisations structurales des différents membres connus de cette famille de peptidases ont révélé un assemblage dodécamériques creux en forme de tétraèdre d'environ 450 kDa. Des études récentes ont montré l'existence de complexes adoptant la même conformation que les TET dans les 3 domaines du vivant. La première partie du travail présenté a permis d'identifier des marqueurs structuraux caractéristiques de l'assemblage tétraédrique afin de déterminer sans ambiguïté l'appartenance de ces complexes à la famille des TET. La seconde partie de l'étude a conduit à élucider la question de la multiplicité des TET chez les Archées hyperthermophile mise en évidence grâce à une étude phylogénétique initiée pendant la thèse. L'étude en co-expression de PhTET2 et PhTET3 révèle que ces aminopeptidases sont capable de former un hétéro-oligomère présentant une activité enzymatique accrue vis-à-vis des homo-oligomères. La dernière partie du travail porte sur les relations oligomérisation-fonction chez les peptidases TET. L'étude d'un mutant de l'oligomérisation de PhTET2 via une stratégie intégrative alliant biochimie, enzymologie, biophysique (SAXS et AUC) et des études in vivo a permis de mettre en évidence un processus d'assemblage contrôlé permettant d'augmenter l'efficacité de la peptidase. Enfin, la méthode de variation de contraste en diffusion de neutrons aux petits angles (SANS) appliqué à l'étude de l'hétéro-oligomère a permis de révéler une topologie rationalise du complexe hétéro-oligomérique favorisant la formations de poches multi-catalytique. L'ensemble de ce travail contribue à mieux comprendre l'importance et le rôle physiologique des machines TETs dans les cellulesProteolysis is a key function in the cell for the maintenance of the proteome integrity, the metabolism and for the regulation of many physiological processes. The thesis work is focused on a family of self-compartmentalized energy-independent cytosolic peptidases discovered in Archaea, the TET aminopeptidases. Three different TET showing contrasted enzymatic specificities co-exist in the cytosol of the hyperthermophilic archaeon Pyrococcus horikoshii, which is the model organism for this study. The structural characterization of the known members of this family shows that they self-assemble in a unique 450 kDa hollow tetrahedral structure . Recent studies have revealed the existence of peptidases complexes that adopt the same conformation in the three domains of life. The first part of this work allowed identifying structural markers to assign without any ambiguity uncharacterized peptidases to the TET family. The second objective of the work was to understand the multiplicity of TET peptidases in hyperthermophilic archaeon that was highlighted by a phylogenomic study presented in this work . The co-expression of PhTET2 and PhTET3 in E. coli revealed that the two proteins form a hetero-oligomeric complex with enhanced enzymatic activity compared to the homo-oligomers. The last part of the work addressed the question of oligomerization-function relationship in TET particles. A mutagenesis strategy was used to slow down the oligomerization process of PhTET2, and, using an integrative strategy combining biochemistry, enzymology, biophysics (SAXS and AUC) and in vivo studies we were able to dissect the oligomerization pathway of the TET particles and to demonstrate that it is a highly controlled process aim to enhance the activity of the peptidases. Finally, the contrast variation technique in small angle neutron scattering studies (SANS) allowed us to unravel the rational topology of the TET hetero-oligomers that favored the formation of multi-catalytic enzymatic pockets in the complex. All theses studies contributed to specify the biological importance of the TET molecular machines in the cells
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Lee, Kyujin C. "Self-assembled lipopeptide prodrug depot for sustaned [sic] release : design and synthesis of peptide glutamic acid dialkylamides, their self-assembly into tubules, and their stability to proteolytic degradation /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/9276.
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Basbous, Hind. "Etudes structurales et propriétés enzymatiques de deux nouvelles aminopeptidases TETs auto-compartimentées chez les archées." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAV016/document.
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Les aminopeptidases représentent un groupe d’enzymes qui possèdent une fonction cellulaire clef dans les mécanismes physiologiques et pathologiques. Elles interviennent dans la cascade enzymatique après l’action des endoprotéases, dans l’homéostasie au travers le renouvellement du pool d’acides aminés, dans le métabolisme énergétique, la régulation de l’activité des peptides bioactifs, la présentation antigénique ainsi dans une diversité de mécanismes pathologiques tels que les maladies neurologiques et les infections virales et parasitaires. Les aminopeptidases TETs sont capables de former des macro-assemblages tétraédriques comprenant douze sous-unités. En vue de mieux comprendre leur fonction biologique et leur mode d'action, nous avons étudié les propriétés fonctionnelles et structurales de deux nouveaux complexes TETs issus d'archées hyperthermophiles. L'archée hyperthermophile Methanocaldococcus jannaschii ne possède qu'une version de TET (MjTET) qui a été produite dans Escherichia coli et purifiée sous forme de dodécamère. La recherche de son activité enzymatique et de ses substrats peptidiques par des tests chromogéniques et fluorogéniques, ainsi que des études par HPLC en phase inverse, montre que cette enzyme est une leucine aminopeptidase activée par le cobalt se distinguant des autres aminopeptidases M42 par son très large spectre d'action qui s'étend aux résidus aromatiques. Une structure complète de cette aminopeptidase a été résolue en combinant la cristallographie (2.4 Å) et la cryo-EM (4,1 Å). L'analyse de la poche de spécificité de MjTET permet de mieux comprendre les bases structurales de la discrimination de substrat chez les TETs. De plus, l'analyse de la structure interne de la particule permet de proposer un nouveau mécanisme de navigation des peptides à l’intérieur des particules tétraédriques de la famille TET.L'archée hyperthermophile Pyrococcus horikoshii comporte trois types de complexes TETs. L'étude d'une protéine présentant ~20 % d'identité avec ces systèmes, nous a permis d'identifier une quatrième version du système TET dans cet organisme : PhTET4. La protéine recombinante a été purifiée. Elle forme un complexe dodécamérique tétraédrique. Les études biochimiques révèlent que l'enzyme possède une spécificité très étroite dirigée exclusivement vers l'hydrolyse des résidus glycines de l'extrémité N-terminale des peptides. De plus, elle estactivée par le nickel. Ces caractéristiques permettent de proposer que, chez les archées, la multiplication et la spécialisation des enzymes TETs seraient associées au caractère hétérotrophes alors que le système des archées autotrophes se réduirait à une TET unique apte à assurer une fonction de « ménage »Aminopeptidases represent a group of enzymes displaying key cellular function inphysiological and pathological mechanisms. They are involved in the enzymatic cascade beyond the action of endoproteases, in homeostasis through the renewal of the amino acid pool, in the energy metabolism, in the regulation of bioactive peptide activities, in the antigen presentation and in a diversity of pathological mechanisms such as neurological diseases as well as viral and parasitic infections. Aminopeptidases TET are able of forming tetrahedral macro-assemblies built by twelve subunits. In order to better understand their biological function and their mode of action, we studied the functional and structural properties of two novel TET complexes derived from hyperthermophilic archaea. The hyperthermophilic archaeon Methanocaldococcus jannaschii has only one version of TET (MjTET) that was produced in Escherichia coli and purified as dodecameric macromolecule. The search for its enzymatic activity and peptide substrates by using chromogenic/fluorogenic assays and reverse phase HPLC studies, demonstrated that this enzyme is a cobalt-activated leucine aminopeptidase, discriminated from other M42 aminopeptidases by its very broad activity spectrum, that extends to aromatic residues. Complete structure of this aminopeptidase was determined by combining X-ray crystallography (2.4 Å) and cryo-electron microscopy (4.1 Å). Analysis of MjTET specificity pocket indicated possible molecular bases for substrate discrimination in TET peptidases. In depth investigation of the particle internal structure allowed to propose a novel peptide trafficking mechanism for the TET family tetrahedral particles. Three types of TET complexes are present in the hyperthermophilic archaea, Pyrococcus horikoshii. The study of an unassigned protein displaying ~20% identity with the PhTETs systems allowed us to identify a fourth version of TET complex in this organism: PhTET4. The recombinant protein was purified. It formed tetrahedral dodecameric complex. Biochemical studies indicated that the enzyme has a very narrow hydrolytic specificity directed exclusively toward the peptide N-terminal glycine residues. In addition, this enzyme is activated by nickel ions. These features allowed proposing that, in archaea, the multiplicity of specialized TET systems could be associated with heterotrophy while unique TET system displaying “housekeeping” function is present in autotrophic organisms
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Mahieu, Emilie. "Étude du mécanisme d’action du protéasome PAN-20S par diffusion de neutrons aux petits angles résolue en temps." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAY073.
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Les protéasomes sont de grands assemblages macromoléculaires ubiquitaires composés d’un complexe catalytique 20S et d’une particule régulatrice comprenant un module AAA-ATPase. Cette machine cellulaire est chargée de dégrader sélectivement les protéines intracellulaires pour permettre le renouvellement du protéome, éliminer les protéines défectueuses et contrôler de nombreuses fonctions biologiques. Le travail de cette thèse avait pour objectif de mettre à jour les mécanismes qui permettent aux complexes AAA-ATPase de déplier sélectivement les protéines substrat et de les transférer à la particule 20S, dans laquelle elles sont détruites. Pour cela, une approche novatrice a été utilisée en combinant la diffusion de neutrons aux petits angles résolue en temps (TR-SANS) avec la spectroscopie de fluorescence permettant de suivre l’activité biochimique. Le protéasome de l’archée hyperthermophile Methanocaldococcus jannaschii, a été utilisé comme système modèle. Il est composé de la protéase 20S et de la particule régulatrice AAA-ATPase PAN. Un variant de la protéine fluorescente GFP a été utilisé comme protéine substrat.Les données obtenues montrent que l’activité de dépliement de PAN génère des formes de GFP dénaturée formant des agrégats. En revanche, l’association avec la particule 20S prévient la formation de ces espèces et indique qu’une fois le dépliement d’une protéine par PAN engagé, les processus de transfert dans le complexe 20S et de dégradation sont étroitement couplés. L’analyse des spectres de diffusion neutronique du substrat GFP montrent que la population de GFP native disparait rapidement au profit des peptides générés par la protéase 20S, comme confirmé par une analyse en spectrométrie de masse. Cela démontre le caractère hautement processif du protéasome. Enfin, deux modes d'action de PAN ont été mis en évidence selon la quantité de protéines à dégrader par rapport au protéasome PAN-20S. Ces travaux permettent de valider expérimentalement un des modèles de fonctionnement du protéasome préalablement proposés et soulignent l’importance d’un contrôle de l’association des protéasomes in vivo. Cette étude met également en valeur l’intérêt de la technique TR-SANS pour étudier la dynamique fonctionnelle de grandes machines cellulairesProteasomes are large ubiquitous macromolecular assemblies composed of a 20S catalytic complex and a regulatory particle containing an AAA-ATPase module. This cellular machine is responsible for selectively degradation of intracellular proteins in order to allow proteome renewal, elimination of defective proteins and control of many biological functions. The objective of this thesis was to reveal the mechanisms by which the AAA-ATPase complexes selectively unfold substrate proteins and translocate them into the 20S particle, where they are destroyed. To this end, an innovative approach was used by combining time-resolved small-angle neutron scattering (TR-SANS) combined with fluorescence spectroscopy to monitor biochemical activity. The proteasome of the hyperthermophilic archaea Methanocaldococcus jannaschii was used as a model system. It is composed of the 20S protease of the regulatory particle AAA-ATPase PAN. A variant of the fluorescent protein GFP was used as a substrate protein.The data obtained show that PAN unfolding activity generates denatured species of GFP forming aggregates. The association with the 20S particle prevents the formation of these species and indicates that once the unfolding of a substrate by PAN is engaged, translocation into the 20S complex and degradation processes are closely coupled. Analysis of the neutron scattering spectra of the GFP substrate reveal that the native GFP population is rapidly disappearing in favor of peptides generated by the 20S protease, as confirmed by mass spectrometric analysis. This demonstrates the highly processive nature of the proteasome. Finally, two modes of action of PAN have been identified depending on the amount of proteins to be degraded compared to the PAN-20S proteasome. This work allows to experimentally validate one of the proteasome function models previously proposed and emphases the importance of controlling the association of proteasomes in vivo. This study also highlights the interest of TR-SANS technique to study the functional dynamics of large cellular machines
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Chintamani, Joshi Anuja. "Influence of the substrate specificity of Mycobacterium tuberculosis ClpX on the transcriptional profile." Thesis, 2018. https://etd.iisc.ac.in/handle/2005/5466.
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Cellular homeostasis in bacteria is maintained by diverse molecular machines. These include several one-component systems (OCS), two- component systems (TCS), chaperone proteins, proteases, proteolytic complexes and transcription factors that regulate protein synthesis and recycling. Protein and oligonucleotide recycling provides a route to clear the cell of aggregated and non-functional bio-molecules thereby mitigating metabolic stress and ensuring bacterial survival. Protein recycling machines in bacteria have been examined in different contexts. These include proteases that function in isolation and chaperone assisted proteases for degradation of specific bio-molecules. The focus of the work reported in this thesis was to understand the mechanism by which proteolytic assemblies influence intracellular signal transduction. This aspect is of particular relevance for the human pathogen Mycobacterium tuberculosis due to its growth features, ability to endure diverse micro-environments inside the host and a pronounced latent phase prior to onset of disease.
M. tuberculosis has several proteases that include FtsH (involved in cell division), Clp proteases- ClpX, ClpC1, ClpP1 and ClpP2 (involved in the maintenance of cellular homeostasis) and the proteasome. Unlike Escherichia coli and Bacillus subtilis, there are no homologues of Lon and HslUV proteases in M. tuberculosis. Indeed, all the Clp proteases in M. tuberculosis are essential. The work described in this thesis reveals the basis by which substrate selectivity is enforced by these chaperone-proteases with direct and indirect repercussions on bacterial adaptation and cellular changes. These studies suggest a link between protein recycling mechanisms and the transcription process suggesting feed-forward and feed-back loops that ensure cellular homeostasis and adaptation to diverse stresses
Book chapters on the topic "Proteolytic assemblies"
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Shahian, Tina, and Charles S. Craik. "Kaposi's Sarcoma Virus Assemblin (Herpesvirus 8-type Assemblin)." In Handbook of Proteolytic Enzymes, 3545–50. Elsevier, 2013. http://dx.doi.org/10.1016/b978-0-12-382219-2.00784-5.
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Gibson, Wade. "Cytomegalovirus Assemblin and Precursor." In Handbook of Proteolytic Enzymes, 3540–45. Elsevier, 2013. http://dx.doi.org/10.1016/b978-0-12-382219-2.00783-3.
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Jupp, Ray, Alison Ritchie, Michael Robinson, Anne Broadhurst, and John Mills. "Epstein-Barr Virus Assemblin." In Handbook of Proteolytic Enzymes, 3552–54. Elsevier, 2013. http://dx.doi.org/10.1016/b978-0-12-382219-2.00786-9.
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McMillan, David, Ray Jupp, John Mills, and John Kay. "Varicella-Zoster Virus Assemblin." In Handbook of Proteolytic Enzymes, 3555–56. Elsevier, 2013. http://dx.doi.org/10.1016/b978-0-12-382219-2.00787-0.
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Jupp, Ray, John Mills, Natalie J. Tigue, and John Kay. "Human Herpesvirus Type 6 Assemblin." In Handbook of Proteolytic Enzymes, 3550–52. Elsevier, 2013. http://dx.doi.org/10.1016/b978-0-12-382219-2.00785-7.
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Kihlberg, Jan. "Glycopeptide synthesis." In Fmoc Solid Phase Peptide Synthesis. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780199637256.003.0012.
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Most eukaryotic proteins, some bacterial and many viral proteins carry structurally diverse carbohydrates that are covalently attached through N- or O-glycosidic bonds to the side chains of asparagine, serine, threonine, hydroxylysine, tyrosine, and hydroxyproline. In nature, N-linked glycoproteins are assembled by post-translational, enzymatic attachment of a common oligosaccharide having the composition Glc3Man9GlcNAc2 to the side chain of asparagine. This saccharide is then modified enzymatically, thereby giving structural variation to the part remote from the protein. However, N-linked glycoproteins have a common pentasaccharide core (Manα3(Manα6)Manβ4GlcNAcβ4GlcNAc) in which the chitobiose moiety (GlcNAcβ4GlcNAc) is bound to asparagine. By contrast, O-linked glycoproteins are built up by sequential attachment of monosaccharides by different enzymes to hydroxylated amino acids in the protein, and therefore no common core is formed. Thus, N-acetyl-α-D-galactosamine attached to serine and threonine is found in mucin secreted from epithelial cells. β-D-Xylosyl serine is found in many proteoglycans, whereas β-D-galactosyl hydroxylysine is common in collagen found in connective tissue. α-L-Fucosyl residues linked to serine and threonine are found in fibrinolytic and coagulation proteins. N-Acetyl-β-D-glucosamine attached to serine and threonine occurs frequently in glycoproteins located in the nucleus and cytoplasm, whereas glycoproteins produced by yeast have α-D-mannosyl residues linked to serine and threonine. Larger structures are usually formed by attachment of additional saccharides to the O-linked 2-4 when found in glycoproteins. Structures 5,10, and 11 can also carry additional monosaccharides. In recent years numerous glycoproteins have been isolated and characterized, but the roles for the protein-bound carbohydrates have only just begun to be unravelled. It is now well established that glycosylation affects both the physiochemical properties and the biological functions of a glycoprotein. For instance, glycosylation has been found to influence uptake, distribution, excretion, and proteolytic stability. It is also known to have important roles in communication between cells and in attachment of bacteria and viruses to the host. Efforts to understand the role of glycosylation of proteins, or to develop glycopeptides as tools in drug discovery and drug design, have led to substantial progress in development of methodology for the synthesis of glycopeptides during the last decades.
Conference papers on the topic "Proteolytic assemblies"
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Medintz, Igor L., Thomas Pons, Kim E. Sapsford, Philip E. Dawson, and Hedi Mattoussi. "Self-assembled quantum dot-bioconjugates: characterization and use for sensing proteolytic activity." In SPIE Defense and Security Symposium, edited by Craig S. Halvorson, Daniel Lehrfeld, and Theodore T. Saito. SPIE, 2008. http://dx.doi.org/10.1117/12.782174.
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Hurley, Jennifer R., Abdul Q. Sheikh, Meredith Beckenhaupt, Cameron Ingram, Andrew Mutchler, and Daria A. Narmoneva. "Self-Assembling Peptide Nanofibers for MMP Delivery and Cardiac Regeneration in Diabetes." In ASME 2011 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2011. http://dx.doi.org/10.1115/sbc2011-53761.
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Diabetes is a serious problem in the United States, afflicting 7.8% of the population with annual medical costs estimated at $116B in 2007 (1). Diabetic cardiomyopathy (DCM) is a cardiovascular complication of diabetes resulting in pathological alterations to the myocardium including circulatory defects, impaired heart muscle contraction, and progressive fibrosis. Cardiac fibrosis is associated with an imbalance between the deposition of the extracellular matrix (ECM) proteins by cardiac fibroblasts and the ECM proteolytic degradation via matrix metalloproteinases (MMPs). Recent studies have demonstrated that in the diabetic heart, expression and activity of MMP-2 are reduced, resulting in increased collagen accumulation and cardiac dysfunction (2). These observations suggest that a MMP-related mechanism may contribute to cardiac fibrosis, and that it may be attenuated through stimulation of native MMP-2 expression or delivery of exogenous MMP-2. Therefore, reduced MMP-2 activity in DCM may represent a novel target for therapeutic treatment (3). To achieve this, a special proteolytically-stable delivery scaffold would be needed, because native ECM is rapidly degraded by MMPs. The goal of this study is to determine if self-assembling peptide nanofibers can be used for long-term (several weeks) MMP delivery and enhancement of cardiac remodeling. This study tests the hypothesis that increased MMP-2 concentration (native or exogenous) in the nanofiber environment will promote matrix remodeling in diabetic cardiac fibroblasts in vitro.
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Verweij, C. L., M. Hart, and H. Pannekoek. "VON WILLEBRAND FACTOR (vWF) PRO-POLYPEPTIDE IS REQUIRED FOR vWF MULTIMER FORMATION." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642831.
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The von Willebrand factor (vWF) is a multimeric plasma glycoprotein synthesized in vascular endothelial cells as a pre-pro-polypeptide with a highly repetitive domain structure, symbolized by the formula:(H)-D1-D2-D'-D3-A1-A2-A3-D4-B1-B2-B3-C1-C2-(0H).A heterologous expression system, consisting of a monkey kidney cell line (C0S-1), transfected with full-length vWF cDNA, is shown to mimic the constitutively, secretory pathway of vWF in endothelial cells. The assembly of pro-vWF into multimers and the proteolytic processing of these structures is found to oro-ceed along the following, consecutive steps. Pro-vWF subunits associate to form dimers, a process that does not involve the pro-polypeptide of pro-vWF. This observation is derived from transfection of C0S-1 cells with vWF cDNA, lacking the genetic information encoding the pro-polypeptide, composed of the domains D1 and D2. Pro-vWF dimers are linked intracellularly to form a regular series of multimeric structures that are secreted and cannot be distinguished from those released constitutively by endothelial cells. The presence of the pro-polypeptide, embedded in pro-vWF, is obligatory for multimerization since the deletion mutant lacking the D1 and D2 domains fails to assemble beyond the dimer stage. It is argued that the D domains are involved in interchain interactions.
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Sadler, J. Evan. "THE MOLECULAR BIOLOGY OF VON WILLEBRAND FACTOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643930.
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Human von Willebrand factor (vWF) is a plasma glycoprotein that is synthesized by endothelial cells and megakaryocytes, and perhaps by syncytiotrophoblast of placenta. The biosynthesis of vWF is very complex, involving proteolytic processing, glycosyla-tion, disulfide bond formation, and sulfation. Mature vWF consists of a single subunit of ∼ 250,000 daltons that is assembled into multimer ranging from dimers to species of over 10 million daltons. vWF performs its essential hemostatic function through several binding interactions, forming a bridge between specific receptors on the platelet surface and components of damaged vascular subendothelial connective tissue. Inherited deficiency of vWF, or von Willebrand disease (vWD), is the most common genetically transmitted bleeding disorder worldwide. The last two years has been a time of very rapid progress in understanding the molecular biology of vWF. Four research groups have independently isolated and sequenced the 9 kilobase full-length vWF cDNA. The predicted protein sequence has provided a foundation for understanding the biosynthetic processing of vWF, and has clarified the relationship between vWF and a 75-100 kilodalton plasma protein of unknown function, von Willebrand antigen II (vWAgll)/ vWAgll is co-distributed with vWF in endothelial cells and platelets, and is deficient in patients with vWD. The cDNA sequence of vWF shows that vWAgll is a rather large pro-peptide for vWF, explaining the biochemical and genetic association between the two proteins. vWF has a complex evolutionary history marked by many separate gene segment duplications. The primary structure of the protein contains four distinct types of repeated domains present in two to four copies each. Repeated domains account for over 90 percent of the protein sequence. This sequence provides a framework for ordering the functional domains that have been defined by protein chemistry methods. A tryptic peptide from the amino-terminus of vWF that overlaps domain D3 binds to factor VIII and also appears to bind to heparin. Peptides that include domain A1 bind to collagens, to heparin, and to platelet glycoprotein Ib. A second collagen binding site appears to lie within domain A3. The vWF cDNA has been expressed in heterologous cells to produce small amounts of functionally and structurally normal vWF, indicating that endothelial cells are not unique in their ability to process and assemble vWF multimers. Site-directed mutagenesis has been used to show that deletion of the propeptide of vWF prevents the formation of multimers. Cloned cDNA probes have been employed to isolate vWF genomic DNA from cosmid and λ-phage libraries, and the size of the vWF gene appears to be ∼ 150 kilobases. The vWF locus has been localized to human chromosome 12p12—pter. Several intragenic RFLPs have been characterized. With them, vWF has been placed on the human genetic linkage map as the most telomeric marker currently available for the short arm of chromosome 12. A second apparently homologous locus has been identified on chromosome 22, but the relationship of this locus to the authentic vWF gene is not yet known. The mechanism of vWD has been studied by Southern blotting of genomic DNA with cDNA probes in a few patients. Three unrelated pedigrees have been shown to have total deletions of the vWF gene as the cause of severe vWD (type III). This form of gene deletion appears to predispose to the development of inhibitory alloantibodies to vWF during therapy with cryoprecipitate. During the next several years recombinant DNA methods will continue to contribute our understanding of the evolution, biosynthesis, and structure-function relationships of vWF, as well as the mechanism of additional variants of vWD at the level of gene structure.