1,721,058 research outputs found
CK2 contribution to the generation of the human phosphoproteome
No full textRecent advances in mass spectrometry technology in combination with the development of innovative experimental strategies have allowed the highly confident characterization of protein phosphorylation on a truly global scale. However, to date, the vast majority of phosphorylation events are still functionally uncharacterized and the link between the phosphorylation site and the kinase(s) responsible for its generation is generally missing.
Primary sequence analysis surrounding the phosphoacceptor site suggests that the main role in the generation of the human phosphoproteome should be accounted to proline-directed protein kinases, found in several sub-branches of the kinome and sharing the essential requirement for a proline at n+1 position; basophilic kinases, very numerous in the human kinome; and acidophilic Ser/Thr protein kinases, a small minority within the kinome and among which protein kinase CK2 play a prominent role. Here we analyze the potential contribution of CK2 considering the entire human phosphoproteome and sub-phosphoproteomes of different functional classes of proteins and sub-cellular compartments. Our analysis suggests that the currently identified CK2 phosphoproteome, consisting in 522 phosphosites, might represent only the tip of the iceberg as it doesn’t reach get the 4% of the potential CK2 phosphosites
A Comparative Analysis and Review of lysyl Residues Affected by Post-translational Modifications
Full text linkPost-translational modification is the most common mechanism of regulating protein function. If phosphorylation is considered a key event in many signal transduction pathways, other modifications must be considered as well. In particular the side chain of lysine residues is a target of different modifications; notably acetylation, methylation, ubiquitylation, sumoylation, neddylation, etc. Mass spectrometry approaches combining highly sensitive instruments and specific enrichment strategies have enabled the identification of modified sites on a large scale. Here we make a comparative analysis of the most representative lysine modifications (ubiquitylation, acetylation, sumoylation and methylation) identified in the human proteome. This review focuses on conserved amino acids, secondary structures preference, subcellular localization of modified proteins, and signaling pathways where these modifications are implicated. We discuss specific differences and similarities between these modifications, characteristics of the crosstalk among lysine post translational modifications, and single nucleotide polymorphisms that could influence lysine post-translational modifications in humans
Mitochondrial tyrosine phosphoproteome: New insights from an up-to-date analysis
No full textTyrosine phosphorylation is a newcomer in the mitochondrial signaling and is currently emerging as an important mechanism for regulating mitochondrial processes. But to what extent? By analyzing an updated draft of the mitochondrial tyrosine phosphoproteome, the following observations can be drawn: more than a hundred mitochondrial proteins undergo tyrosine phosphorylation, phosphotyrosine proteins are distributed in each of the submitochondrial compartments, and mitochondrial tyrosine phosphorylated proteins are involved in a variety of functions as metabolism (electron transport chain, Krebs cycle, fatty acid and amino acid metabolism), solute and protein transport, mitochondrial translation machinery, quality protein assessment, oxidative stress, apoptosis, fission, and other. This large and varied collection suggests that tyrosine phosphorylation could be a widespread mechanism in modulating mitochondrial functions. Moreover the in silico model is here used to explore potential effects of tyrosine phosphorylation on selected mitochondrial proteins pointing out some future perspectives in this field
La qualità della governance in ambito rurale: quali indicatori e quali strumenti per misurarla?
No full textLa recente crisi economica e finanziaria che ha investito l’economia mondiale ha portato a scenari instabili, da un lato con effetti negativi - colpendo e penalizzando il settore primario in molteplici aspetti - dall’altro anche con effetti positivi - stimolando la riflessione e l’attenzione a nuove e più efficaci forme di governance nelle politiche agricole e in generale nell’ambito dello sviluppo rurale. Per una serie di fattori, tra cui ad esempio la crescente domanda di trasparenza e responsabilità espressa dalla società civile in merito all’operato dei soggetti pubblici, nonché degli attori del mondo finanziario ed economico internazionale di fronte alle sfide poste dalla globalizzazione e dai cambiamenti climatici, tali forme innovative di governance si basano sempre più sulla partecipazione di una pluralità di attori nei processi decisionali, sulla condivisione delle responsabilità, su meccanismi distributivi di costi e benefici conseguenti alle decisioni prese, sulla trasparenza e lo scambio delle informazioni, sul coordinamento intra- ed inter-settoriale, sulla creazione di reti e relazioni di interdipendenza, reciprocità e fiducia. Ambiti applicativi preferenziali di queste nuove forme di governance sono, in Italia come in Europa, le politiche ambientali e quelle di sviluppo rurale.
Il lavoro, che intende dare un contributo di riflessione funzionale alla costruzione di un quadro teorico-concettuale sul tema della governance delle risorse naturali e dei territori rurali, è organizzato in tre parti. Nella prima si cerca di meglio delineare il concetto stesso di governance ed in particolare di governance partecipativa, illustrando brevemente le iniziative che, soprattutto a scala internazionale, stanno cercando di monitorarne e valutarne la qualità: Nella seconda parte è presentato lo stato dell’arte nelle procedure di selezione dei Gruppi di Azione Locale (GAL) e dei Programmi di Sviluppo Locale (PSL) (approccio LEADER) in Italia. Nella terza parte, infine, si presentano: i) il quadro di riferimento teorico-concettuale qui appositamente sviluppato di una metodologia di valutazione della qualità della governance in grado di affiancare elementi innovativi (partecipazione, trasparenza, responsabilità, ecc.) ad altri più consolidati e tradizionali (efficacia, efficienza); ii) i risultati della comparazione effettuata tra le procedure di selezione dei GAL/PSL adottate da alcune Regioni italiane ed il set di valutazione della qualità della governance proposto. Si approfondisce inoltre la coerenza tra il metodo qui delineato e le metodologie proposte dalla Commissione Europea (Questionario Valutativo Comune, QVC) per la valutazione delle politiche di sviluppo rurale 2007-2013. Il contributo si chiude con alcune riflessioni conclusive e raccomandazioni
Linear and cyclic peptides as substrates for lyn tyrosine kinase
No full textTwo Tyr residues are supposed to play a crucial role in the regulation of protein tyrosine kinases of the Src family. Autophosphorylation of Src Tyr416 correlates with enzyme activation, while phosphorylation of C-terminal Tyr527 by Csk gives rise to inactive forms of Src kinases. It has previously been demonstrated that the Src-like tyrosine kinase expressed by the oncogene lyn displays a particularly high affinity (Km20 μm) toward the dimeric linear and cyclic derivatives of the heptapeptide H-Glu-Asp-Asn-Glu-Tyr-Thr-Ala-OH which reproduces the main autophosphorylation site of most of the Src enzymes. Under the experimental conditions used only one Tyr residue of the dimeric sequence can be phosphorylated [P. Ruzza, A. Calderan, B. Filippi, B. Blondi, A. Donella Deana, L. Cesaro, L. A. Pinna & G. Borin (1995) Int. J. Peptide Protein Res. 45, 529-539]. The present study addresses the problem of the efficiency displayed by Lyn towards the two Tyr residues located at positions 5 and 12 of the dimeric peptide. To this purpose, two tetradecapeptides were synthesized by the classical solution method, each containing one of the two Tyr residues alternatively replaced by Phe, and the corresponding univocal cyclic form. A possible correlation between the different structural properties induced by the modifications of the native sequence and the ability of the peptides to act as Lyn substrates was noted. The kinetic data obtained indicate that Lyn phosphorylates the residues located at different positions in the two linear analogues differently. In particular, while the Tyr5, Phe12 derivative presents a Kmvalue similar to those obtained for the dimeric linear and cyclic unmodified analogues, the Kmvalue of the Phe5, Tyr12 derivative is two-fold higher than those found for the above-mentioned peptides. Moreover, as previously reported for the linear and cyclic dimeric forms of the native sequence, in the mono-tyrosine containing series of dimers the still conformationally flexible cyclic derivative shows a phosphorylation efficiency two-fold higher than those found for the linear derivatives. © 1998 European Peptide Society and John Wiley & Sons, Ltd
Dissecting the Role of K61/K59 Residue in VPS4 Functions
No full textESCRTs (Endosomal Sorting Complexes Required for Transport) are required for the formation of the intraluminal vesicles in the multivesicular bodies and are involved in other topologically similar processes such as cytokinesis, nuclear envelope sealing and viral egress. The final complex ESCRT-III is disassembled by the recruitment and activation of the AAA-ATPase VPS4 to the endosomal membranes. This recruitment is due to the binding of VPS4 N-terminal MIT with MIM1 and MIM2 domains present in the CHMPs proteins. By analyzing different cellular membrane remodeling events in which VPS4 is involved, here we provide evidence that the K61 residue, mapping within the MIT domain of VPS4B (K59 in VPS4A), is involved in VPS4 functioning. Posttranslational modifications of this residue might modulate MIT-MIM2 binding affinity and, as a consequence, VPS4 functions
La qualità della governance: prime riflessioni sull’autovalutazione dei GAL LEADER.
No full textIl contributo si pone il principale obiettivo di presentare un approfondimento sulle tecniche di valutazione dello sviluppo
rurale in Europa, con particolare riferimento alla valutazione
della governance locale. E’ noto che un’adeguata valutazione della qualità della governance in ambito rurale può essere un utile strumento di supporto nella formulazione, attuazione e revisione delle politiche pubbliche. Tuttavia, di fronte ai limiti riscontrati negli attuali strumenti di monitoraggio e valutazione delle politiche e dei progetti di sviluppo locale dei territori rurali, in particolare nel Common Monitoring and Evaluation Framework - CMEF sta
sempre più emergendo la necessità di disporre di strumenti
nuovi, che permettano di fare una valutazione puntuale a livello
locale ad integrazione dei quella ampia e mediata a livello
regionale, nazionale o addirittura comunitario. In queste tipologie
di strumenti, l’oggetto della valutazione dovrebbe divenire lo
stesso agente di sviluppo animatore del territorio rurale, ovvero il
soggetto attuatore delle politiche, piuttosto che la politica in sé.
Ciò consentirebbe a tali soggetti (GAL, Enti Parco, Organizzazioni non profit o Enti territoriali di varia natura) di avere indicazioni più efficaci e funzionali alle decisioni da prendere in quanto più adeguati al contesto locale ed orientati al miglioramento delle modalità di gestione interna e comunicazione/networking: in altre parole, della governance che il soggetto attua nel contesto locale.La messa a punto di sistemi di autovalutazione ha avuto un qualche sviluppo nell’ambito delle iniziative LEADER dove, nel periodo di programmazione 2000-2006, sono stati “testati” alcuni metodi. Il contributo presenta alcune riflessioni preliminari alla messa a punto di un sistema di auto-valutazione dei GAL nei LEADER basato su un set innovativo di indicatori della qualità della governance locale. Tale sistema di auto-valutazione potrebbe validamente integrare e completare gli attuali strumenti comunitari di valutazione e monitoraggio dello sviluppo rurale ed avere implicazioni operative direttamente sui soggetti locali attuatori delle politiche
Extraordinary pleiotropy of protein kinase CK2 revealed by weblogo phosphoproteome analysis
No full textA weblogo has been generated from the sequences surrounding 433 Ser/Thr protein residues whose phosphorylation by protein kinase CK2 had been previously validated ("bona fide" CK2 phosphosites). This has been compared to the weblogo extracted from 2275 putative CK2 phosphosites displaying the motif pS/pT-x1-x2-D/E/pS (where x1 not=P) present in the human phosphoElm database including 10899 naturally occurring phosphosites. The two weblogos are strikingly similar supporting the notion that indeed the 2275 putative sites (accounting for 20.9% of the whole phosphoproteome they belong to), or at least the great majority of these are generated by CK2. This conclusion has been corroborated by the random validation of 8 of such putative CK2 sites (belonging to 5 different proteins) as real targets of CK2 in vitro and/or in cells, leading to the inclusion into the repertoire of bona fide CK2 targets of 5 new entries, namely: oxidative stress-responsive kinase-1, anthrax toxin receptor 1, hepatoma derived growth factor, EpsinR and BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like
Distribution of protein disulfide isomerase in rat liver mitochondria
Full text linkHere we report the localization of protein disulphide isomerase (PDI) in the mitochondrial compartments, comparing it with that of thioredoxin reductase. The latter enzyme is present mostly in the matrix, whereas PDI is located at the level of the outer membrane. We characterize the different submitochondrial fractions with specific marker enzymes. PDI, whether isolated from whole mitochondria or from purified outer membranes, exhibits the same electrophoretic mobility, indicating identical molecular masses. Moreover, immunoblot analysis with monoclonal anti-PDI antibody shows immunoreactivity only with the microsomal PDI, indicating the specificity of the mitochondrial isoform. The significance of these findings is discussed with reference to the potential role of PDI and thioredoxin reductase in regulating the mitochondrial functions dependent on the thiol–disulphide transition
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