Search results for "Motif"
showing 10 items of 290 documents
Characterization of the interaction between Actinin-Associated LIM Protein (ALP) and the rod domain of α-actinin
2009
Abstract Background The PDZ-LIM proteins are a family of signalling adaptors that interact with the actin cross-linking protein, α-actinin, via their PDZ domains or via internal regions between the PDZ and LIM domains. Three of the PDZ-LIM proteins have a conserved 26-residue ZM motif in the internal region, but the structure of the internal region is unknown. Results In this study, using circular dichroism and nuclear magnetic resonance (NMR), we showed that the ALP internal region (residues 107–273) was largely unfolded in solution, but was able to interact with the α-actinin rod domain in vitro, and to co-localize with α-actinin on stress fibres in vivo. NMR analysis revealed that the ti…
Sorting signals in the cytosolic tail of plant p24 proteins involved in the interaction with the COPII coat.
2004
The ability of the cytosolic tail of a plant p24 protein to bind COPI and COPII subunits from plant and animal sources in vitro has been examined. We have found that a dihydrophobic motif in the -7,-8 position (relative to the cytosolic carboxy-terminus), which strongly cooperates with a dilysine motif in the -3,-4 position for COPI binding, is required for COPII binding. In addition, we show that COPI and COPII coat proteins from plant cytosol compete for binding to the sorting motifs in these tails. Only in the absence of the dilysine motif in the -3,-4 position or after COPI depletion could we observe COPII binding to the p24 tail. This competition is not observed when using rat liver cy…
Irredundant tandem motifs
2014
Eliminating the possible redundancy from a set of candidate motifs occurring in an input string is fundamental in many applications. The existing techniques proposed to extract irredundant motifs are not suitable when the motifs to search for are structured, i.e., they are made of two (or several) subwords that co-occur in a text string s of length n. The main effort of this work is studying and characterizing a compact class of tandem motifs, that is, pairs of substrings {m1, m2} occurring in tandem within a maximum distance of d symbols in s, where d is an integer constant given in input. To this aim, we first introduce the concept of maximality, related to four specific conditions that h…
Entropic Profiles, Maximal Motifs and the Discovery of Significant Repetitions in Genomic Sequences
2014
The degree of predictability of a sequence can be measured by its entropy and it is closely related to its repetitiveness and compressibility. Entropic profiles are useful tools to study the under- and over-representation of subsequences, providing also information about the scale of each conserved DNA region. On the other hand, compact classes of repetitive motifs, such as maximal motifs, have been proved to be useful for the identification of significant repetitions and for the compression of biological sequences. In this paper we show that there is a relationship between entropic profiles and maximal motifs, and in particular we prove that the former are a subset of the latter. As a furt…
Algorithms for Graph and Network Analysis: Clustering and Search of Motifs in Graphs
2019
In this article we deal with problems that involve the analysis of topology in graphs modeling biological networks. In particular, we consider two important problems: (i) Network clustering, aiming at finding compact subgraphs inside the input graph in order to isolate molecular complexes, and (ii) searching for motifs, i.e., sub-structures repeated in the input network and presenting high significance (e.g., in terms of their frequency). We provide a compact overview of the main techniques proposed in the literature to solve these problems.
Icarus and Daedalus in Toni Morrison's "Song of Solomon"
2012
In Song of Solomon Toni Morrison rewrites the legend of the Flying Africans and the Myth of Icarus to create her own Myth. Her depiction of the black hero’s search for identity has strong mythical overtones. Morrison rescues those elements of mythology black culture which are still relevant to blacks and fuses them with evident allusions to Greek mythology. She reinterprets old images and myths of flight, the main mythical motif in the story. Her Icarus engages on an archetypical journey to the South, to his family past, led by his Daedalic guide, on which he finally recovers his ancestral ability to fly. His flight signals a spiritual epiphany in the hero’s quest for self-definition in the…
Challenging the Victorian Nuclear Family Myth: The Incest Trope in Guillermo del Toro’s Crimson Peak
2020
espanolLa literatura (neo)victoriana ofrece conceptualizaciones contradictorias de la familia nuclear, ya que generalmente gira en torno a hogares tradicionales heteroparentales pero los presenta como fragmentados y profundamente disfuncionales. La pelicula Crimson Peak (2015) del director Guillermo del Toro se basa en tres motivos recurrentes en la ficcion gotica (neo) victoriana, los traumas domesticos, la familia disfuncional y lo sobrenatural. Mi objetivo principal es explorar como Del Toro utiliza la trama del incesto para subvertir las visiones preconcebidas e idealizadas sobre la familia victoriana. En primer lugar, analizo la casa ancestral y la figura materna como origen de los tra…
The Biosynthesis of Rare Homo-Amino Acid Containing Variants of Microcystin by a Benthic Cyanobacterium
2019
Microcystins are a family of chemically diverse hepatotoxins produced by distantly related cyanobacteria and are potent inhibitors of eukaryotic protein phosphatases 1 and 2A. Here we provide evidence for the biosynthesis of rare variants of microcystin that contain a selection of homo-amino acids by the benthic cyanobacterium Phormidium sp. LP904c. This strain produces at least 16 microcystin chemical variants many of which contain homophenylalanine or homotyrosine. We retrieved the complete 54.2 kb microcystin (mcy) gene cluster from a draft genome assembly. Analysis of the substrate specificity of McyB1 and McyC adenylation domain binding pockets revealed divergent substrate specificity …
Asymmetric synthesis of cyclopentanes bearing four contiguous stereocenters via an NHC-catalyzed Michael/Michael/esterification domino reaction.
2016
An NHC-catalyzed Michael/Michael/esterification domino reaction via homoenolate/enolate intermediates for the asymmetric synthesis of tetrasubstituted cyclopentanes is described.
Multifunctionality of F-rich nucleoporins
2020
Nucleoporins (Nups) represent a range of proteins most known for composing the macromolecular assembly of the nuclear pore complex (NPC). Among them, the family of intrinsically disordered proteins (IDPs) phenylalanine-glycine (FG) rich Nups, form the permeability barrier and coordinate the high-speed nucleocytoplasmic transport in a selective way. Those FG-Nups have been demonstrated to participate in various biological processes besides nucleocytoplasmic transport. The high number of accessible hydrophobic motifs of FG-Nups potentially gives rise to this multifunctionality, enabling them to form unique microenvironments. In this review, we discuss the multifunctionality of disordered and …