An evolutionary and functional assessment of regulatory network motifs | Genome Biology | Full Text
Thomas D, Surdin-Kerjan Y: Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 1997, 61: 503- ... Types of motifs of order n = 2 and n = 3 for the mixed transcription and protein-protein network. The motifs shown here are ... The motifs for the mixed networks were investigated in .. The dynamics of motifs has been thoroughly investigated in vitro ... Motif occurrence in yeast. The network graph of the occurrences of motifs for S. cerevisiae illustrates the fact that most of ...https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-4-r35
SLiMSuite & SeqSuite: open-source bioinformatics in Python: May 2012
Many protein-protein interactions are mediated by Short Linear Motifs (SLiMs): short stretches of proteins (5-15 amino acids ... Nuc Acids Res 38:W534;  Davey NE et al. (2011): SLiMSearch 2.0: biological context for short linear motifs in proteins. Nuc ... CompariMotif : Motif-motif comparison tool. *SLiMMaker (coming soon): Simple tool for converting aligned peptides or SLiM ... Motif predictions ((Q)SLiMFinder/SLiMPrints/SLiMPred) will be able to be searched directly against known motifs (CompariMotif) ...http://seqsuite.blogspot.com/2012/05/
400 amino acids). Two iterations on SPTR37_10f were required to reach convergence, at which point a true set comprising 32 ... FINAL MOTIF SETS TYPE3IMSPROT1 Length of motif = 23 Motif number = 1 Type III IMS protein family motif I - 2 PCODE ST INT ... SCAN HISTORY SPTR37_10f 2 45 NSINGLE INITIAL MOTIF SETS TYPE3IMSPROT1 Length of motif = 23 Motif number = 1 Type III IMS ... Length of motif = 16 Motif number = 4 Type III IMS protein family motif IV - 1 PCODE ST INT HIAIGIYFNPEIAPAP SPAS_SHIFL 260 26 ...http://22.214.171.124/cgi-bin/dbbrowser/PRINTS/DoPRINTS.pl?cmd_a=Display&qua_a=/Full&fun_a=Code&qst_a=TYPE3IMSPROT
215 amino acids. This domain is shared by a number of other proteins, including the rat FIT-1M precursor, the murine ST2L ... FINAL MOTIF SETS INTRLKN1R1F1 Length of motif = 29 Motif number = 1 Interleukin-1 receptor type I family motif I - 2 PCODE ST ... SCAN HISTORY SPTR39_15f 2 50 NSINGLE INITIAL MOTIF SETS INTRLKN1R1F1 Length of motif = 29 Motif number = 1 Interleukin-1 ... Length of motif = 14 Motif number = 6 Interleukin-1 receptor type I family motif VI - 1 PCODE ST INT IKQKHGAIRWSGDF IL1R_HUMAN ...http://126.96.36.199/cgi-bin/dbbrowser/PRINTS/DoPRINTS.pl?cmd_a=Display&qua_a=/Full&fun_a=Code&qst_a=INTRLKN1R1F
PfEMP1-DBL1α amino acid motifs in severe disease states of Plasmodium falciparum malaria | PNAS
... severe motifs; M, mild motifs; C, cerebral malaria motifs; N, severe malaria NUD motifs; NS, nonsevere malaria NUD motifs; R, ... Specific PfEMP1-DBL1α amino acid motifs correlated with rosetting and severe malaria, with motif location corresponding to ... Amino acids involved in receptor binding are indicated by blue dots, and amino acids essential for binding are represented by ... PfEMP1-DBL1α amino acid motifs in severe disease states of Plasmodium falciparum malaria. Johan Normark, Daniel Nilsson, Ulf ...http://www.pnas.org/content/104/40/15835
The Amino Acid Motif L/IIxxFE Defines a Novel Actin-Binding Sequence in PDZ-RhoGEF
Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica
Amino acid motifs in P. indica In order to screen the genome of P. indica for known and unknown motifs in the amino acid ... A search for motifs (Table S12 and S13) in the amino acid sequences of these heterogeneous proteins identified a group of 25 ... amino acid permeases, transmembrane amino acid transporter proteins, nucleobase cation symporters, ABC-2 type transporters, and ... 1) Secreted proteins were predicted using TargetP and SignalP as described in material and methods, amino acid motifs in P. ...http://pubmedcentralcanada.ca/pmcc/articles/PMC3192844/
Imperfect interface of Beclin1 coiled-coil domain regulates homodimer and heterodimer formation with Atg14L and UVRAG.
Amino Acid Motifs. Amino Acid Sequence. Apoptosis Regulatory Proteins / metabolism*. Autophagy. Class III Phosphatidylinositol ... Another prominent feature of the Beclin 1 CC structure is the unusually high composition of charged amino acid residues, as ... Beclin 1 self-association is independent of autophagy induction by amino acid deprivation and rapamycin treatment. J. Cell ... are directly involved in Beclin 1-Atg14L interaction because mutating these amino acids to hydrophobic leucine residue nearly ...http://www.biomedsearch.com/nih/Imperfect-interface-Beclin1-coiled-coil/22314358.html
A survey of machine learning methods for secondary and supersecondary protein structure prediction. - NextBio article
Amino Acid Motifs Artificial Intelligence Computational Biology Models, Molecular Protein Structure, Secondary Proteins ...http://www.nextbio.com/b/search/article.nb?id=22987348
A Screen for New Trithorax Group Genes Identified little imaginal discs, the Drosophila melanogaster Homologue of Human...
... a bipartite nuclear localization signal is found at amino acids 1599-1616. Each of these amino acid motifs is found in human ... This domain has a previously described amino acid motif called ARID (AT-rich interaction domain; Herrscheret al. 1995). Among ... Amino acid motifs were determined using the Profilescan program and PsortII programs. Protein alignments were performed on the ... The protein contains a number of amino acid motifs found in both trithorax and Polycomb group genes. It contains an N-terminal ...http://www.genetics.org/content/156/2/645
Effects of recombinant N-terminal proteins on rates of | Open-i
Protein Interaction Domains and Motifs/physiology*. Minor. *Actin Cytoskeleton/genetics/metabolism. *Amino Acid Motifs/genetics ... Mentions: To assess whether the motif or C1 affected rates of force activation in addition to their effects on steady-state ... Mentions: To assess whether the motif or C1 affected rates of force activation in addition to their effects on steady-state ... These results suggest that the C1 domain plus the motif constitute a functional unit of MyBP-C that can activate the thin ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC2571974_jgp1320575f07&req=4
Tau GSTs involved in regulation of leaf abscission by comparison the gene profiling of Me GSTs in various abscission-promoting...
The motif lengths with 11 and 50 amino acids long were confirmed by MEME analysis (Fig. 2; Additional file 3: Figure S1). In ... The amino acid motifs and phylogenetic analyses indicated that MeGSTs were divided into 9 classes. The global expression ... Further, the phylogenetic tree and amino acid motifs prediction and analysis were carried out. A globe microarray analysis was ... the TCHQD GST genes have motifs 1, 4, and 6; the GHR GST genes have motifs 4 and 6; the EF1Bγ GST genes have motifs 1, 4, 9, 10 ...https://link.springer.com/article/10.1186%2Fs12863-018-0627-6
Silencing SUMO E2 enzyme Ubc9 represses DENV replicatio | Open-i
Amino Acid Motifs. *Amino Acid Sequence. *Animals. *Cell Line. *Cells, Cultured. *Dengue/genetics/metabolism/virology ... we found that the SUMO acceptor sites are located in the N-terminal domain of NS5 and that a putative SUMO-interacting motif ( ... we found that the SUMO acceptor sites are located in the N-terminal domain of NS5 and that a putative SUMO-interacting motif ( ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC4836324_zjv9990915840001&req=4
Overexpression of eYFP-PIAS4 disrupts SUMO pathway home | Open-i
Amino Acid Motifs. *Amino Acid Sequence. *Cell Line. *DNA Replication. *DNA, Viral ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC4836348_zjv9990916200004&req=4
Stabilin-1 localizes to endosomes and the trans-Golgi network in human macrophages and interacts with GGA adaptors.
Amino Acid Motifs/immunology, Antigens; CD/immunology, Brefeldin A/pharmacology, Carrier Proteins/immunology/metabolism, Cell ...http://uu.diva-portal.org/smash/record.jsf?pid=diva2:96016
Glycogen synthase kinase 3beta interaction protein functions as an A-kinase anchoring protein - Publikationsserver der...
Amino Acid Motifs/physiology. MESH. Cell Line, Tumor. MESH. Cyclic AMP-Dependent Protein Kinases/metabolism. MESH. ... Our bioinformatics and peptide array screening approaches based on this signature motif identified GSKIP (glycogen synthase ... of the interactions between the dimerization and docking domain and various PKA-binding domains yielded a generalized motif ...https://epub.uni-regensburg.de/30633/
Amphioxus (Branchiostoma floridae) has orthologs of vertebrate odorant receptors | BMC Evolutionary Biology | Full Text
Key amino acid motifs. To identify amino acid motifs common in vertebrate and B. floridae ORs, we constructed an alignment of ... By exposing conserved amino acid motifs and testing the ability of those motifs to discriminate between ORs and non-OR GPCRs, ... from which a list of candidate amino acid motifs was generated. To determine whether these motifs were present in ORs, non-ORs ... Conserved amino acid motifs have previously been noted in alignments of human, mouse and zebrafish OR sequences [13, 27, 30, 31 ...https://0-bmcevolbiol-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1471-2148-9-242
The diverse evolutionary pattern of ESEs and ESSs in as | Open-i
Amino Acid Motifs. *Animals. *DNA Mutational Analysis. *Enhancer Elements, Genetic. *Gene Silencing ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC3091315_gb-2009-10-11-r120-3&req=4
The distribution of mIMRs in the immature Gag protein [ | Open-i
The gag gene of HIV-1 [GenBank:K03455] was selected for the study because its protein motifs and structural components are well ... Nucleic Acid Conformation*. *Protein Conformation*. *Tandem Repeat Sequences/genetics*. *gag Gene Products, Human ... The gag gene of HIV-1 [GenBank:K03455] was selected for the study because its protein motifs and structural components are well ... The distribution of IMRs and their relationship to structural and functional motifs in the protein that they translate, suggest ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC2211468_1743-422X-4-113-1&req=4
Conserved expression patterns associated with functiona | Open-i
Conserved expression patterns associated with functional binding site motif variants (BSMVs).The y-axis of each plot is the ... Amino Acid Motifs. *Binding Sites. *Computational Biology/methods. *Genome, Fungal. *Genomics. *Models, Statistical ... Bottom Line: To accomplish this, we statistically detect motif variants with effects that differ among environments.We find ... Bottom Line: To accomplish this, we statistically detect motif variants with effects that differ among environments.We find ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC3285675_pone.0032274.g003&req=4
A 20 amino acid motif in the β subunit loop is sufficient for clustering. A , CD4-β loop chimeras were generated with either ... First, we tested CD4-chimeras containing the first (amino acids 333-406) or second halves (aa 407-469) of the β loop (Fig. 2). ... By making deletions in the β loop we defined a 20 amino-acid sequence that is sufficient for clustering. The sequence contains ... Using chimeric proteins consisting of CD4 fused to each of the AChR subunit intracellular loops, we identify a 20 amino acid ...http://www.jneurosci.org/content/28/45/11468
Heme regulates B-cell differentiation, antibody class switch, and heme oxygenase-1 expression in B cells as a ligand of Bach2 |...
Regulation by heme of mitochondrial protein transport through a conserved amino acid motif. Science 1993;259(5094):522-525. ... Bach1 possesses at least 4 Cys-Pro motifs (CP motifs)21,22 involved in heme-binding. Heme binds to Bach1 to inhibit its DNA ... 5 Although amino acid residues involved in the heme binding represented by the 432-nm peak remain to be identified, our ... Involvement of heme regulatory motif in heme-mediated ubiquitination and degradation of IRP2. Mol Cell 2005;19(2):171-181. ...http://www.bloodjournal.org/content/117/20/5438?ijkey=2a319d5cc8692e839765f28e4f62f5d43c7eeea1&keytype2=tf_ipsecsha&sso-checked=true
Malleability of protein folding pathways : a simple reason for complex behaviour.
Amino Acid Motifs, Models; Molecular, Protein Conformation, Protein Folding, Proteins/*chemistry/*metabolism, Signal ...http://su.diva-portal.org/smash/record.jsf?faces-redirect=true&language=sv&searchType=SIMPLE&query=&af=%5B%5D&aq=%5B%5B%5D%5D&aq2=%5B%5B%5D%5D&aqe=%5B%5D&pid=diva2%3A188993&noOfRows=50&sortOrder=author_sort_asc&sortOrder2=title_sort_asc&onlyFullText=false&sf=all
Inhibition of the binding activity of recombinant PB2 w | Open-i
Amino Acid Motifs/genetics. *Amino Acid Sequence. *Animals. *Binding Sites/genetics. *Cell Line, Tumor ... In contrast, anacardic acid and garcinol drastically inhibited the interaction, and concentrations of anacardic acid greater ... In contrast, anacardic acid and garcinol drastically inhibited the interaction, and concentrations of anacardic acid greater ... p , 0.01; DMSO versus anacardic acid. †, p , 0.05 and ††, p , 0.01; DMSO versus garcinol. Mentions: One HAT, p300/cAMP-response ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC4155666_zbc0411495550004&req=4
Frontiers | Microbial effectors target multiple steps in the salicylic acid production and signaling pathway | Plant Science
Among these, salicylic acid signaling is an important pathway because of its ability to trigger plant cell death. As biotrophic ... Here we review the strategies prokaryotic pathogens have developed to target salicylic acid biosynthesis and signaling, and ... Here we review the strategies prokaryotic pathogens have developed to target salicylic acid biosynthesis and signaling, and ... they have evolved efficient strategies to downregulate salicylic acid signaling by virulence effectors, which can be proteins ...https://www.frontiersin.org/articles/10.3389/fpls.2015.00349/full