Search results for "Motif"

LRP1 modulates APP trafficking along early compartments of the secretory pathway

2008

The amyloid beta peptide (A beta) is a central player in Alzheimer's disease (AD) pathology. A beta liberation depends on APP cleavage by beta- and gamma-secretases. The low density lipoprotein receptor related protein 1 (LRP1) was shown to mediate APP processing at multiple steps. Newly synthesized LRP1 can interact with APP, implying an interaction between these two proteins early in the secretory pathway. We wanted to investigate whether LRP1 mediates APP trafficking along the secretory pathway, and, if so, whether it affects APP processing. Indeed, the early trafficking of APP within the secretory pathway is strongly influenced by its interaction with the C-terminal domain of LRP1. The …

Different conformations of nascent polypeptides during translocation across the ER membrane

2000

Abstract Background In eukaryotic cells, proteins are translocated across the ER membrane through a continuous ribosome-translocon channel. It is unclear to what extent proteins can fold already within the ribosome-translocon channel, and previous studies suggest that only a limited degree of folding (such as the formation of isolated α-helices) may be possible within the ribosome. Results We have previously shown that the conformation of nascent polypeptide chains in transit through the ribosome-translocon complex can be probed by measuring the number of residues required to span the distance between the ribosomal P-site and the lumenally disposed active site of the oligosaccharyl transfer…

A novel RNA-binding motif in influenza A virus non-structural protein 1.

1997

The solution NMR structure of the RNA-binding domain from influenza virus non-structural protein 1 exhibits a novel dimeric six-helical protein fold. Distributions of basic residues and conserved salt bridges of dimeric NS1(1-73) suggest that the face containing antiparallel helices 2 and 2′ forms a novel arginine-rich nucleic acid binding motif.

Pyruvate dehydrogenase specific T cells in primary biliary cirrhosis show restricted antigen recognition sites

2002

:  Background/Aims: The aim was to characterise the antigen recognition sites of the variable T cell receptor α-chain (TCRAV) and β-chain (TCRBV) of T cells specific to the pyruvate dehydrogenase (PDC) in primary biliary cirrhosis. Methods: In 21 PDC-specific T cell clones isolated from five patients we analysed TCRAV and TCRBV usage by RT-PCR and sequenced the CDR3 regions. Results: Preferential expression of the TCR elements BV6 (6 clones), BV12 (4 clones) and BV1 (3 clones), and frequent usage of the joining elements JB2.3 and JB2.1 were seen. Analysis of the α chain revealed rearrangement of AV2 in 7 clones (35%) and AV7 in 3 clones, however, distribution of the joining elements was het…

A Closed Book: Opacity of the Human Self in Mullā Ṣadrā

2014

Mullā Ṣadrā Shīrāzī (d. 1636) subscribes at large to the Avicennian view according to which the human subject is always and fully aware of herself. At the same time, his eschatology hinges on the Qur’ānic motive of the soul as a closed book that is first opened on the Final Day, that is, on the idea that each soul’s share in the afterlife should be understood as the full revelation of the soul’s true nature to itself. The two ideas thus have seemingly contradictory entailments: the soul is fully aware of and transparent to itself, but at the same time it has aspects that can remain opaque to it, at least in this life. The task of this paper is to investigate whether Ṣadrā can coherently hol…

Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells

2013

AbstractPluripotency is maintained by both known and unknown transcriptional regulatory networks. In the present study, we have identified Zfp819, a KRAB-zinc finger protein, as a novel pluripotency-related factor and characterized its role in pluripotent stem cells. We show that Zfp819 is expressed highly in various types of pluripotent stem cells but not in their differentiated counterparts. We identified the presence of non-canonical nuclear localization signals in particular zinc finger motifs and identified them as responsible for the nuclear localization of Zfp819. Analysis of the Zfp819 promoter region revealed the presence of a transcriptionally active chromatin signature. Moreover,…

Interaction of syntenin-1 and the NG2 proteoglycan in migratory oligodendrocyte precursor cells.

2008

Migration of oligodendrocyte precursors along axons is a necessary prerequisite for myelination, but little is known about underlying mechanisms. NG2 is a large membrane proteoglycan implicated in oligodendrocyte migration. Here we show that a PDZ domain protein termed syntenin-1 interacts with NG2 and that syntenin-1 is necessary for normal rates of migration. The association of syntenin-1 with NG2, identified in a yeast two-hybrid screen, was confirmed by colocalization of both proteins within processes of oligodendroglial precursor cells and by coimmunoprecipitation from cell extracts. Syntenin-1 also colocalizes with NG2 in "co-capping" assays, demonstrating a lateral association of bot…

Author response: Inhibitory activities of short linear motifs underlie Hox interactome specificity in vivo

2015

Flexible pattern discovery with (extended) disjunctive logic programming

2005

The post-genomic era showed up a wide range of new challenging issues for the areas of knowledge discovery and intelligent information management. Among them, the discovery of complex pattern repetitions in string databases plays an important role, specifically in those contexts where even what are to be considered the interesting pattern classes is unknown. This paper provides a contribution in this precise setting, proposing a novel approach, based on disjunctive logic programming extended with several advanced features, for discovering interesting pattern classes from a given data set.

MMGBSA As a Tool To Understand the Binding Affinities of Filamin–Peptide Interactions

2013

Filamins (FLN) are large dimeric proteins that cross-link actin and work as important scaffolds in human cells. FLNs consist of an N-terminal actin-binding domain followed by 24 immunoglobulin-like domains (FLN1-24). FLN domains are divided into four subgroups based on their amino acid sequences. One of these subgroups, including domains 4, 9, 12, 17, 19, 21, and 23, shares a similar ligand-binding site between the β strands C and D. Several proteins, such as integrins β2 and β7, glycoprotein Ibα (GPIbα), and migfilin, have been shown to bind to this site. Here, we computationally estimated the binding free energies of filamin A (FLNa) subunits with bound peptides using the molecular mechan…