3,597 research outputs found
Mutations in disordered proteins as early indicators of nucleic acid changes triggering speciation
No full textIntrinsically disordered proteins are characterized by unusual sequence composition, structural flexibility, and functional spectra. These properties play an essential role in fostering protein evolution and in the formation of complex cellular pathways, especially in multicellular organisms. In this study, we analyze the role of different structural variants of proteins in speciation processes. Firstly, we separate human and mouse proteomes (taken as a reference) in three variants of disorder: ordered proteins (ORDPs), structured proteins with intrinsically disordered protein regions (IDPRs), and intrinsically disordered proteins (IDPs). Secondly, we compare the DNA divergence with the corresponding protein divergence, by confronting human and mouse coding sequences (separated in ORDPs, IDPRs, and IDPs) with their homologs from 26 eukaryotes. As a general rule, we find that IDPs phenotypically diverge earlier than ORDPs and IDPRs. ORDPs diverge later but are phenotypically more reactive to nucleotide mutations than IDPRs and IDPs. We suggest that IDPs may be involved in the early stages of the speciation process, likely connected to their functional spectra, mainly related to nucleic acid binding and transcription factors. In contrast, ORDPs may be essential in accelerating further phenotypic divergence
The codon frustration index as a new metric for mRNA stability, translation efficiency, and rates of protein synthesis
No full textTaking the human genome as a case of study, we propose a new classification of codons based only on two genomic information. We use the relative synonymous codon usage (RSCU) as a measure of non-uniform usage of synonymous codons. Similarly, we introduce here the relative gene frequencies of cognate tRNAs (RGFCt) to quantify the non-uniform availability of cognate tRNAs in each family of synonymous codons. Using these two quantities, we define two general groups of codons: non-frustrated codons, whose usage in the coding sequences is in proportion to the expected cognate tRNA levels, and frustrated codons, which do not satisfy this proportionality. With this decoding for every codon, we defined the Codon Frustration Index (CFI) as the net frustration of a gene, normalized for its length. Notably, we find that CFI correlates very well with other independent measures of CUB and a high content of non-frustrated codons increases both translation efficiency and mRNA stability. Finally, we show that genes with either a high content of frustrated or of non-frustrated codons are differentially enriched in specific functional classes that typically comprise nucleic acid binding proteins, mRNA processing factors, RNA helicase, and in several transcription factors
Variants of intrinsic disorder: structural characterization
No full textIn a recent study, we have introduced an operational classification of the human proteome in three variants of disorder: ordered proteins (ORDPs), structured proteins with intrinsically disordered protein regions (IDPRs), intrinsically disordered proteins (IDPs). That classification was useful in functionally separating IDPRs from IDPs, which up until now have been generally considered as a whole. In this study, we corroborate this distinction by considering different physical-chemical and structural properties. Both ORDPs and IDPRs are enriched in order-promoting amino acids, whereas only IDPs show an enrichment in disordered-promoting amino acids. Consistently, ORDPs and IDPRs are preferentially located in the ordered phase of the charge-hydropathy plot, whereas IDPs are widespread over the disordered phase. We introduce the mean packing - mean pairwise energy (MP-MPE) plane to structurally characterize these variants even in the absence of a structural model. As expected for well-packed proteins, a negative linear correlation is observed between MP and MPE for ORDPs and IDPRs, whereas IDPs break this linear dependence. Finally, we find that IDPs have a more extended conformation as measured by the scaling law between the radius of gyration and the length of these proteins, and accordingly they have higher solubility and accessible surface area than ORDPs and IDPRs. Overall, our results confirm the relevance of our operational separation of IDPRs from IDPs and provide further validation of our criteria to separate IDPs from the rest of human proteome
Intrinsically disordered proteins and structured proteins with intrinsically disordered regions have different functional roles in the cell
No full textMany studies about classification and the functional annotation of intrinsically disordered proteins (IDPs) are based on either the occurrence of long disordered regions or the fraction of disordered residues in the sequence. Taking into account both criteria we separate the human proteome, taken as a case study, into three variants of proteins: i) ordered proteins (ORDPs), ii) structured proteins with intrinsically disordered regions (IDPRs), and iii) intrinsi- cally disordered proteins (IDPs). The focus of this work is on the different functional roles of IDPs and IDPRs, which up until now have been generally considered as a whole. Previous studies assigned a large set of functional roles to the general category of IDPs. We show here that IDPs and IDPRs have non-overlapping functional spectra, play different roles in human diseases, and deserve to be treated as distinct categories of proteins. IDPs enrich only a few classes, functions, and processes: nucleic acid binding proteins, chromatin bind- ing proteins, transcription factors, and developmental processes. In contrast, IDPRs are spread over several functional protein classes and GO annotations which they partly share with ORDPs. As regards to diseases, we observe that IDPs enrich only cancer-related pro- teins, at variance with previous results reporting that IDPs are widespread also in cardiovas- cular and neurodegenerative pathologies. Overall, the operational separation of IDPRs from IDPs is relevant towards correct estimates of the occurrence of intrinsically disordered pro- teins in genome-wide studies and in the understanding of the functional spectra associated to different flavors of protein disorder
Co-evolution between codon usage and protein-protein interaction in bacteria
No full textWe study the correlation between the codon usage bias of genetic sequences and the network features of protein protein interaction (PPI) in bacterial species. We use PCA techniques in the space of codon bias indices to show that genes with similar patterns of codon usage have a significantly higher probability that their encoded proteins are functionally connected and interacting. Importantly, this signal emerges when multiple aspects of codon bias are taken into account at the same time. The present study extends our previous observations on E. coli over a wide set of 34 bacteria. These findings could allow for future investigations on the possible effects of codon bias on the topology of the PPI network, with the aim of improving existing bioinformatics methods for predicting protein interactions
Il contributo di Sergio Torsello alla renaissance salentina del primo quindicennio del 2000
No full textQuesto contributo mira a descrivere le tre “anime” di Sergio Torsello – Direttore Artistico del Festival La Notte della Taranta, Consulente Scientifico dell’Istituto Diego Carpitella, e Mediatore Culturale tra e per i talenti artistici del suo territorio. Il punto di partenza della narrazione è un articolo di Sergio Torsello, pubblicato nel 2011 in un volume di cui l’autore della narrazione è stato curatore. L’autore sottolinea la stretta connessione tra le tre anime di Sergio Torsello, che emerge non solo dal suo articolo del 2011 ma anche dalle numerose interazioni avvenute tra Sergio Torsello e l’autore. La descrizione del rilievo scientifico della figura di Sergio Torsello è sicuramente parziale, circoscritta nel tempo (gli 8 anni, dal 2007 al 2015 in cui ha interagito con l’autore) e nello spazio (inteso come insieme di argomenti delle loro conversazioni scientifiche e culturali). Ma rende merito del cruciale contributo di Sergio Torsello alla renaissance culturale salentina degli anni dal 2001 al 2015.This contribution aims to describe the three “souls” of Sergio Torsello – Artistic Director of “La Notte della Taranta” Festival, Scientific Consultant of “Diego Carpitella” Institute, and Cultural Mediator
between and for the artistic talents of his territory. The starting point of the description is an article by Sergio Torsello, published in 2011 in a book of which the author of the description was the editor. The author highlights the close connection between the three souls of Sergio Torsello, which emerges not only from the above-mentioned article, but also from the numerous interactions between Sergio Torsello and the author. The description of the scientific significance of Sergio Torsello’s figure is certainly partial, limited in time (the 8 years, from 2007 to 2015, in which he interacted with the author) and in space (in terms of set of topics of their scientific and cultural conversations). But it gives merit to Sergio Torsello’s key contribution to the cultural renaissance of Salento in the years from 2001 to 2015
Stochastic Generalized Nash Equilibrium-Seeking in Merely Monotone Games
No full textWe solve the stochastic generalized Nash equilibrium (SGNE) problem in merely monotone games with expected value cost functions. Specifically, we present the first distributed SGNE-seeking algorithm for monotone games that require one proximal computation (e.g., one projection step) and one pseudogradient evaluation per iteration. Our main contribution is to extend the relaxed forward–backward operator splitting by the Malitsky (Mathematical Programming, 2019) to the stochastic case and in turn to show almost sure convergence to an SGNE when the expected value of the pseudogradient is approximated by the average over a number of random samples.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Team Sergio GrammaticoTeam Bart De Schutte
Sergio Bettini e la critica d’arte
No full textOn the occasion of the publication of two books about Sergio Bettini’s works (unpublished studies, conference proceedings and critical apparatus) the author analyzes the scientific production of this scholar during his life (1930-1986). Furtherly this essay analyzes the great scholar’s relationship with the School of Wien and first of all his deep connection with all European different critical and comparative points of view
Guest Editorial: Introduction to IEEE Control Systems Letters Special Section on Multi-Agent Coordination for Energy Systems: From Model Based to Data-Driven Methods
No full textEditorialGreen Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Team Sergio GrammaticoTeam Bart De Schutte
Cromatismo, ritmo, memoria: sulla narrativa di Sergio Atzeni
No full textSergio Atzeni’s works are many and really heterogeneous, both in style and contents. But if we dig up deeply into his texts, we discover that the currents followed by the author are always the same, and that texts that are apparently different have actually significant common aspects.Le opere di Sergio Atzeni sono numerose e molto eterogenee, sia nello stile che nei contenuti. Ma se andiamo a scavare nel profondo, ci rendiamo conto che i filoni seguiti dall’autore sono sempre gli stessi, e che esiti testuali apparentemente distinti hanno in realtà importanti aspetti in comune
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