Identifying Protein Short Linear Motifs by Position-Specific Scoring Matrix

2016 ◽  
pp. 206-214
Author(s):  
Chun Fang ◽  
Tamotsu Noguchi ◽  
Hayato Yamana ◽  
Fuzhen Sun
Keyword(s):  
Position Specific Scoring Matrix ◽  
Short Linear Motifs ◽  
Scoring Matrix ◽  
Linear Motifs

scholarly journals Short Linear Motifs Characterizing Snake Venom and Mammalian Phospholipases A2

Toxins ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 290
Author(s):  
Caterina Peggion ◽  
Fiorella Tonello
Keyword(s):  
Snake Venom ◽  
Protein Interactions ◽  
Biological Properties ◽  
Protein Protein Interactions ◽  
Sequence Alignments ◽  
Toxic Activity ◽  
Short Linear Motifs ◽  
Phospholipases A2 ◽  
Group I ◽  
Linear Motifs

Snake venom phospholipases A2 (PLA2s) have sequences and structures very similar to those of mammalian group I and II secretory PLA2s, but they possess many toxic properties, ranging from the inhibition of coagulation to the blockage of nerve transmission, and the induction of muscle necrosis. The biological properties of these proteins are not only due to their enzymatic activity, but also to protein–protein interactions which are still unidentified. Here, we compare sequence alignments of snake venom and mammalian PLA2s, grouped according to their structure and biological activity, looking for differences that can justify their different behavior. This bioinformatics analysis has evidenced three distinct regions, two central and one C-terminal, having amino acid compositions that distinguish the different categories of PLA2s. In these regions, we identified short linear motifs (SLiMs), peptide modules involved in protein–protein interactions, conserved in mammalian and not in snake venom PLA2s, or vice versa. The different content in the SLiMs of snake venom with respect to mammalian PLA2s may result in the formation of protein membrane complexes having a toxic activity, or in the formation of complexes whose activity cannot be blocked due to the lack of switches in the toxic PLA2s, as the motif recognized by the prolyl isomerase Pin1.

Position-specific scoring matrix and hidden Markov model complement each other for the prediction of conopeptide superfamilies

2013 ◽  
Vol 1834 (4) ◽  
pp. 717-724 ◽  
Author(s):  
Dominique Koua ◽  
Silja Laht ◽  
Lauris Kaplinski ◽  
Reto Stöcklin ◽  
Maido Remm ◽  
...  
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Hidden Markov ◽  
Position Specific Scoring Matrix ◽  
Scoring Matrix

scholarly journals Resources to Discover and Use Short Linear Motifs in Viral Proteins

2020 ◽  
Vol 38 (1) ◽  
pp. 113-127 ◽  
Author(s):  
Peter Hraber ◽  
Paul E. O’Maille ◽  
Andrew Silberfarb ◽  
Katie Davis-Anderson ◽  
Nicholas Generous ◽  
...  
Keyword(s):  
Viral Proteins ◽  
Short Linear Motifs ◽  
Linear Motifs

scholarly journals Inhibitory activities of short linear motifs underlie Hox interactome specificity in vivo

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Manon Baëza ◽  
Séverine Viala ◽  
Marjorie Heim ◽  
Amélie Dard ◽  
Bruno Hudry ◽  
...  
Keyword(s):  
Cell Fate ◽  
Drosophila Embryo ◽  
Traditional Role ◽  
Hox Proteins ◽  
Short Linear Motifs ◽  
Wide Range ◽  
Mouse Species ◽  
Inhibitory Activities ◽  
Linear Motifs

Hox proteins are well-established developmental regulators that coordinate cell fate and morphogenesis throughout embryogenesis. In contrast, our knowledge of their specific molecular modes of action is limited to the interaction with few cofactors. Here, we show that Hox proteins are able to interact with a wide range of transcription factors in the live Drosophila embryo. In this context, specificity relies on a versatile usage of conserved short linear motifs (SLiMs), which, surprisingly, often restrains the interaction potential of Hox proteins. This novel buffering activity of SLiMs was observed in different tissues and found in Hox proteins from cnidarian to mouse species. Although these interactions remain to be analysed in the context of endogenous Hox regulatory activities, our observations challenge the traditional role assigned to SLiMs and provide an alternative concept to explain how Hox interactome specificity could be achieved during the embryonic development.

scholarly journals A comprehensive motifs-based interactome of the C/EBPα transcription factor

2020 ◽  
Author(s):  
Evelyn Ramberger ◽  
Valeria Sapozhnikova ◽  
Elisabeth Kowenz-Leutz ◽  
Karin Zimmermann ◽  
Nathalie Nicot ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Protein Interaction ◽  
Intrinsically Disordered Proteins ◽  
Arginine Methylation ◽  
Disordered Proteins ◽  
List Type ◽  
Short Linear Motifs ◽  
Intrinsically Disordered ◽  
Linear Motifs ◽  
Factor C

AbstractThe pioneering transcription factor C/EBPα coordinates cell fate and cell differentiation. C/EBPα represents an intrinsically disordered protein with multiple short linear motifs and extensive post-translational side chain modifications (PTM), reflecting its modularity and functional plasticity. Here, we combined arrayed peptide matrix screening (PRISMA) with biotin ligase proximity labeling proteomics (BioID) to generate a linear, isoform specific and PTM-dependent protein interaction map of C/EBPα in myeloid cells. The C/EBPα interactome comprises promiscuous and PTM-regulated interactions with protein machineries involved in gene expression, epigenetics, genome organization, DNA replication, RNA processing, and nuclear transport as the basis of functional C/EBPα plasticity. Protein interaction hotspots were identified that coincide with homologous conserved regions of the C/EBP family and revealed interaction motifs that score as molecular recognition features (MoRF). PTMs alter the interaction spectrum of multi-valent C/EBP-motifs to configure a multimodal transcription factor hub that allows interaction with multiple co-regulatory components, including BAF/SWI-SNF or Mediator complexes. Combining PRISMA and BioID acts as a powerful strategy to systematically explore the interactomes of intrinsically disordered proteins and their PTM-regulated, multimodal capacity.Key pointsIntegration of proximity labeling and arrayed peptide screen proteomics refines the interactome of C/EBPα isoformsHotspots of protein interactions in C/EBPα mostly occur in conserved short linear motifsInteractions of the BAF/SWI-SNF complex with C/EBPα are modulated by arginine methylation and isoform statusThe integrated experimental strategy suits systematic interactome studies of intrinsically disordered proteins

scholarly journals Using position specific scoring matrix and auto covariance to predict protein subnuclear localization

2009 ◽  
Vol 02 (01) ◽  
pp. 51-56 ◽  
Author(s):  
Rong-Quan Xiao ◽  
Yan-Zhi Guo ◽  
Yu-Hong Zeng ◽  
Hai-Feng Tan ◽  
Hai-Feng Tan ◽  
...  
Keyword(s):  
Position Specific Scoring Matrix ◽  
Subnuclear Localization ◽  
Scoring Matrix ◽  
Auto Covariance
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