Kunes S, Chu T, Chiu M, Zhang E. A C-terminal motif targets hedgehog to axons, coordinating assembly of the Drosophila eye and brain. Developmental Cell [Internet]. 2006;10 (5) :635-46.
Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at http://elm.eu.org/ provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes ,1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a Bar Code format, ...
The purpose of this study was to investigate the blood stage of the malaria causing parasite, Plasmodium falciparum, to predict potential protein interactions between the parasite merozoite and the host erythrocyte and design peptides that could interrupt these predicted interactions. We screened the P. falciparum and human proteomes for computationally predicted short linear motifs (SLiMs) in cytoplasmic portions of transmembrane proteins that could play roles in the invasion of the erythrocyte by the merozoite, an essential step in malarial pathogenesis. We tested thirteen peptides predicted to contain SLiMs, twelve of them palmitoylated to enhance membrane targeting, and found three that blocked parasite growth in culture by inhibiting the initiation of new infections in erythrocytes. Scrambled peptides for two of the most promising peptides suggested that their activity may be reflective of amino acid properties, in particular, positive charge. However, one peptide showed effects which were ...
Many important interactions of proteins are facilitated by short, linear motifs (SLiMs) within a proteins primary sequence. Our aim was to establish robust methods for discovering putative functional motifs. The strongest evidence for such motifs is obtained when the same motifs occur in unrelated proteins, evolving by convergence. In practise, searches for such motifs are often swamped by motifs shared in related proteins that are identical by descent. Prediction of motifs among sets of biologically related proteins, including those both with and without detectable similarity, were made using the TEIRESIAS algorithm. The number of motif occurrences arising through common evolutionary descent were normalized based on treatment of BLAST local alignments. Motifs were ranked according to a score derived from the product of the normalized number of occurrences and the information content. The method was shown to significantly outperform methods that do not discount evolutionary relatedness, when ...
1] Tompa P (2011) Unstructural biology coming of age. Curr Opin Struct Biol 21: 419; [2] Babu MM et al. (2011) Intrinsically disordered proteins: regulation and disease. Curr Opin Struct Biol 21:432; [3] Diella F et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13:6580; [4] Davey NE et al. (2012) Attributes of short linear motifs. Mol Biosyst 8:268; [5] Davey NE, Trave G & Gibson TJ (2011) How viruses hijack cell regulation. Trends Biochem Sci 36:159; [6] Davey NE, Edwards RJ & Shields DC (2010) Computational identification and analysis of protein short linear motifs. Front Biosci 15:801; [7] Davey NE, Shields DC & Edwards RJ (2006): SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res. 34:3546; [8] Edwards RJ, Davey NE & Shields DC (2007): SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2:e967; ...
Shop Leucine-rich PPR motif-containing protein ELISA Kit, Recombinant Protein and Leucine-rich PPR motif-containing protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of pathway knowledge.
Many important regulatory interactions are mediated by short linear motif sequences, which are often embedded in disordered protein regions. These interactions tend to be transient, and therefore pose special experimental challenges. In order to develop precise tools for the manipulation and study of such interactions, accurate structural models are needed. However, due to weak binding affinity and the considerable flexibility of the peptide, structural modeling of peptide-mediated interactions presents a considerable challenge. In my talk I will present an overview of our research on peptide-mediated interactions. I will describe Rosetta FlexPepDock, the suite of protocols that we have developed, and applied, for the structure-based characterization and manipulation of peptide-mediated interactions. FlexPepDock is guided by observations of peptide binding strategies revealed from solved complex crystal structures. Efficient but focused sampling strategies have opened the way to model these ...
so sum1tar is basically summary 1 of the target motifs, those are the motifs i got from the motifenrichment analysis on my sequences using the motifenrich function inside the PWMenrich package. So i use scanWithPWM to get the highest score and i am not sure if the highest one represents the optimal position?. So after i have got the position , i hope to plot the sequence with the motif on top of the sequence somehow, i have tried using substring from the biostring package but only able to plot the sequences. So second question is about plotting the motif or highlighting the motif detected with the sequence. after we have detected the motifs, would there be any ways that i could highlight the motifs ? because so far i am only able to make a ranking table in the in the window and highlight the rough position just like the one in the manual. However i would like to see every single base pair with highlighted motifs in the sequence. The third quesiton is about pairwise alignment and motif anlysis, ...
We have extracted an extensive collection of recurrent structural motifs (RSMs), which consist of sequentially non-contiguous structural motifs (4-6 residues), each of which appears with very similar conformation in three or more mutually unrelated protein structures. We find that the proteins in our set are covered to a substantial extent by the recurrent non-contiguous structural motifs, especially the helix and strand regions. Computational alanine scanning calculations indicate that the average folding free energy changes upon alanine mutation for most types of non-alanine residues are higher for amino acids that are present in recurrent structural motifs than for amino acids that are not. The non-alanine amino acids that are most common in the recurrent structural motifs, i.e., phenylalanine, isoleucine, leucine, valine and tyrosine and the less abundant methionine and tryptophan, have the largest folding free energy changes. This indicates that the recurrent structural motifs, as we define them,
The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). For |10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear mot …
BACKGROUND: Large datasets of protein interactions provide a rich resource for the discovery of Short Linear Motifs (SLiMs) that recur in unrelated proteins. However, existing methods for estimating the probability of motif recurrence may be biased by the size and composition of the search dataset, such that p-value estimates from different datasets, or from motifs containing different numbers of non-wildcard positions, are not strictly comparable. Here, we develop more exact methods and explore the potential biases of computationally efficient approximations.. RESULTS: A widely used heuristic for the calculation of motif over-representation approximates motif probability by assuming that all proteins have the same length and composition. We introduce pv, which calculates the probability exactly. Secondly, the recently introduced SLiMFinder statistic Sig, accounts for multiple testing (across all possible motifs) in motif discovery. However, it approximates the probability of all other possible ...
The motivating idea behind most discussions on motifs is the possibility of capturing the essential logic of genetic regulation by a small set of interaction circuits performing some specific functional tasks. While this hypothesis is, in principle, experimentally testable, experimental and theoretical work has hitherto considered essentially motifs in isolation, that is, excised from the biological environment in which the motifs instances are embedded.. We studied in detail the role of motifs in the case of the best-documented genetic sub-networks and biological functions where such motifs are found. In most cases, motifs do not seem to have a central regulatory role in the biological processes associated with each occurrence. The list of examples where enough biological information is available is, of course, limited, and further examples may subvert this picture. At the moment, it is a fact that all the examples studied highlight the high level of integration of different regulatory ...
SCAN HISTORY OWL25_2 2 300 NSINGLE SPTR37_9f 2 125 NSINGLE INITIAL MOTIF SETS ADENOVSFIBRE1 Length of motif = 11 Motif number = 1 ADV fibre protein motif I - 1 PCODE ST INT EDDFNPVYPYE FIBP_ADE40 7 7 SDSFNPVYPYE FIBP_ADE07 26 26 EDDFNPVYPYG FIBP_ADE08 8 8 EDDFNPVYPYG FIBP_ADE09 8 8 EDTFNPVYPYD FIBP_ADE05 8 8 STSFNPVYPYE FIBP_ADE03 8 8 PANFDPVYPYD FIBP_ADECG 9 9 PANYDPVYPYD CA2FIBER 9 9 ADENOVSFIBRE2 Length of motif = 13 Motif number = 2 ADV fibre protein motif II - 1 PCODE ST INT DIPFITPPFASSN FIBP_ADE40 23 5 QHPFINPGFISPN FIBP_ADE07 42 5 NIPFLTPPFVSSN FIBP_ADE08 24 5 NIPFLTPPFVSSD FIBP_ADE09 24 5 TVPFLTPPFVSPN FIBP_ADE05 25 6 QHPFINPGFISPD FIBP_ADE03 24 5 PKPSTQPPFFNDR FIBP_ADECG 21 1 PGSSTQPPFFNNK CA2FIBER 21 1 ADENOVSFIBRE3 Length of motif = 15 Motif number = 3 ADV fibre protein motif III - 1 PCODE ST INT NGALTLKLGTGLNID FIBP_ADE40 57 21 GGSLQLKVGGGLTID FIBP_ADE07 76 21 NQNVSLKVGGGLTLQ FIBP_ADE08 58 21 NGNVSLKVGGGLTLQ FIBP_ADE09 58 21 NGMLALKMGNGLSLD FIBP_ADE05 59 21 SGSLQLKVGSGLTVD ...
This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, namely a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. [provided by RefSeq, Jul 2008 ...
Inspired by the main element role of super-helical motifs in molecular self-organization, several tandem heptad repeat peptides were used as building blocks to form well-ordered supramolecular nano-assemblies. structures at the nanoscale5,6,7. However, the formation of assemblies by such short peptides is limited mainly to -sheet business of the peptide motifs in the formed nanostructures8,9,10,11. While these assemblies offers remarkable mechanical, optical, piezolelctric and semiconductive proprieties, they lack the precise orientation of amino-acid residues needed for directed intermolecular business and specific interactions with target molecules such as DNA or other biopolymers12,13. Indeed, in many biological systems, the recognition of DNA is usually facilitated by ordered super-helical structural motifs14,15,16. This super-helical business commonly comprised of two or more Tegobuvir individual -helices that interact with each other via hydrophobic facets present in protein surfaces and ...
mouse Slo2 protein: a type of sodium-activated K+ channel, possess a typical PDZ binding motif at the carboxy-terminal end; NP_780671
This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly. In full display mode, each motif occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the + strand is shown.. The track may be configured to search for any short sequence of 2 - 30 bases in length. Sequences may include IUPAC ambiguity codes. To change the motif, open the tracks description page (by clicking the track control label or the mini-button to the left of the track), then type a new sequence into the text box.. To see how to create a bed file of the short match data see this mailing list question here.. ...
This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly. In full display mode, each motif occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the + strand is shown.. The track may be configured to search for any short sequence of 2 - 30 bases in length. Sequences may include IUPAC ambiguity codes. To change the motif, open the tracks description page (by clicking the track control label or the mini-button to the left of the track), then type a new sequence into the text box.. To see how to create a bed file of the short match data see this mailing list question here.. ...
This track shows all occurrences of a selected short motif within the displayed position range of the assembly sequence. It is useful for finding oligonucleotides, restriction sites, or other recurring short sequences within the assembly. In full display mode, each motif occurrence is labeled by the strand on which the match is located, followed by the starting coordinate of the match. In cases where the input motif sequence is identical to its reverse complement, only the match on the + strand is shown.. The track may be configured to search for any short sequence of 2 - 30 bases in length. Sequences may include IUPAC ambiguity codes. To change the motif, open the tracks description page (by clicking the track control label or the mini-button to the left of the track), then type a new sequence into the text box.. ...
6 K in this function is the background entropy corrected for sample size, approximately 2 for E. coli (4), as was calculated in the example above. The frequencies, fi, are determined as in the example above from the aligned sequences of the prototype group for the given motif; the relative frequencies for the occurrence of each of the four bases are determined separately for each position of the motif. Fopt is the frequency found for the consensus base at a given position, and fobs is the frequency at which the base in the sequence of interest is found to occur in the same position of the prototype group.. A computer program was written that takes sequence as input, evaluates this function at each position within a window corresponding to the size of the motif of interest by using the prototype groups frequencies, divides the range of resultant index values into six qualitative levels from very good to very bad (attempts with 10 levels yielded no better performance), and codes the result in ...
SCAN HISTORY SPTR37_10f 2 45 NSINGLE INITIAL MOTIF SETS TYPE3IMSPROT1 Length of motif = 23 Motif number = 1 Type III IMS protein family motif I - 1 PCODE ST INT TEKPTPKKLKDAAKKGQSFKFKD SPAS_SHIFL 5 5 TEKPTKKRLEDSAKKGQSFKSKD SPAS_SALTY 6 6 TEQPTPKKIRDARKKGQVAKSKE YSCU_YERPS 6 6 TEQPTEKKLRDGRKEGQVVKSIE SSAU_SALTY 5 5 TEQPTDKKLEDAHRDGETAKSAD HRPN_BURSO 6 6 TELPSAKKIQKAREEGNVPKSME FLHB_HELPY 7 7 TEEPSAKKLSDARAKGDVIKSAD Q45997 11 11 TEAPSEKKISDATEKGNVPFSRE O54243 11 11 TEAPTPHRLEKAREEGQIPRSRE FLHB_ECOLI 9 9 TELPTDQKKQKAREEGRVLKSTE FLHB_BORBU 26 26 TEKATPKQIRDAREKGQVGQSQD O85098 5 5 SHGATPKKLSDARKRGQIPRSSD Y4YO_RHISN 9 9 TYPE3IMSPROT2 Length of motif = 19 Motif number = 2 Type III IMS protein family motif II - 1 PCODE ST INT DFVIEFILYMKDMMMDKQE SPAS_SHIFL 196 168 DAIAEYFLTMKDMKMDKEE SPAS_SALTY 197 168 DYAFEYYQYIKELKMSKDE YSCU_YERPS 202 173 DYSFQYYKIRKDLKMSKDD SSAU_SALTY 201 173 DFGIQRWLFIRDHRMSKDE HRPN_BURSO 203 174 DLAIKRRQYTNSLKMTKQE FLHB_HELPY 204 174 DYFWQRMRFMNRMRMTLQE Q45997 209 175 ...
Residues within a conserved amino acid motif of domains 1 and 4 of VCAM-1 are required for binding to VLA-4.. Journal of Cell Biology. 125:215-222. 1994 ...
View mouse Trim21 Chr7:102557921-102565486 with: phenotypes, sequences, polymorphisms, proteins, references, function, expression
View mouse Trim33 Chr3:103279293-103358775 with: phenotypes, sequences, polymorphisms, proteins, references, function, expression
Feature map marking the locations of 4G-, 3G- and 2G-containing motif occurrences in the G-rich motif group identified in the upstream regions of the organellar
For three decades, sequence logos are the de facto standard for the visualization of sequence motifs in biology and bioinformatics. Reasons for this success story are their simplicity and clarity. The number of inferred and published motifs grows with the number of data sets and motif extraction algorithms. Hence, it becomes more and more important to perceive differences between motifs. However, motif differences are hard to detect from individual sequence logos in case of multiple motifs for one transcription factor, highly similar binding motifs of different transcription factors, or multiple motifs for one protein domain. Here, we present DiffLogo, a freely available, extensible, and user-friendly R package for visualizing motif differences. DiffLogo is capable of showing differences between DNA motifs as well as protein motifs in a pair-wise manner resulting in publication-ready figures. In case of more than two motifs, DiffLogo is capable of visualizing pair-wise differences in a tabular form.
Batten disease is a neurodegenerative disorder resulting from mutations in CLN3, a polytopic membrane protein, whose predominant intracellular destination in nonneuronal cells is the lysosome. The topology of CLN3 protein, its lysosomal targeting mechanism, and the development of Batten disease are poorly understood. We provide experimental evidence that both the N and C termini and one large loop domain of CLN3 face the cytoplasm. We have identified two lysosomal targeting motifs that mediate the sorting of CLN3 in transfected nonneuronal and neuronal cells: an unconventional motif in the long C-terminal cytosolic tail consisting of a methionine and a glycine separated by nine amino acids [M(X)9G], and a more conventional dileucine motif, located in the large cytosolic loop domain and preceded by an acidic patch. Each motif on its own was sufficient to mediate lysosomal targeting, but optimal efficiency required both. Interestingly, in primary neurons, CLN3 was prominently seen both in ...
In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which also appears in a variety of other molecules. Motifs do not allow us to predict the biological functions: they are found in proteins and enzymes with dissimilar functions. Because the relationship between primary structure and tertiary structure is not straightforward, two biopolymers may share the same motif yet lack appreciable primary structure similarity. In other words, a structural motif does not have to be associated with a sequence motif. Also, the existence of a sequence motif does not necessarily imply a distinctive structure. In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal double helical structure. ...
The chromo domain was originally identified as a protein sequence motif common to the Drosophila chromatin proteins, Polycomb (Pc) and heterochromatin protein 1 [HP1; Paro and Hogness (1991) Proc. Natl. Acad. Sci. USA, 88, 263-267; Paro (1990) Trends Genet., 6, 416-421]. Here we describe a second chromo domain-like motif in HP1. Subsequent refined searches identified further examples of this chromo domain variant which all occur in proteins that also have an N-terminally located chromo domain. Due to its relatedness to the chromo domain, and its occurrence in proteins that also have a classical chromo domain, we call the variant the chromo shadow domain. Chromo domain-containing proteins can therefore be divided into two classes depending on the presence, for example in HP1, or absence, for example in Pc, of the chromo shadow domain. We have also found examples of proteins which have two classical chromo domains. The Schizosaccharomyces pombe SWI6 protein, involved in repression of the silent ...
Red Hat Motif 2.1 for Linux Intel-compatible computers is the full OSF/Motif development system. As with previous versions of Red Hat Motif, Red Hat Motif 2.1 will enable you to use your Intel-compatible PC computer running Linux as a UNIX(r) Motif based workstation.For developers, Motif 2.1 makes creation of software applications and custom widgets simple. The many toolkit enhancements, new widgets, and UIL improvements allow you to port Motif-based applications easily across a variety of platforms.For end users, Red Hat Motif 2.1 improves the interface performance of their Motif-based applications. The virtual screen support unclutters their workspace by providing alternate locations for chosen windows, while providing greater consistency with PC environments.Red Hat Motif 2.1 New Features: Thread safe libraries Widget printing support Internationalization enhancements for vertical text, on-the-spot input and user defined characters for Asian languages See Red Hat Motif 2.1 Intel on the Store Page
Coronaviruses, including SARS-CoV-2, are proposed to use either the endocytic or non-endosomal pathway for cell entry (46). Our study provides biophysical evidence for the functionality of SLiMs in the cytoplasmic tails of ACE2 and integrin β3, which provide possible molecular links between the established (ACE2) and putative (integrin beta3) SARS-CoV-2 receptors and mediators of endocytosis and autophagy. Our finding that an endocytic AP2 μ2 binding motif exists in the ACE2 C-terminus and that such binding is negatively regulated by Tyr781 phosphorylation supports the possibility of clathrin-dependent endocytosis of SARS-CoV-2 upon receptor binding. It will, of course, be necessary to assess the biological relevance of the ACE2-AP2 μ2 interaction, particularly in light of its low affinity. Concerning the latter, we note that while affinities of AP2 core complexes for endocytic sorting signals are reported in the nanomolar range, measured KD values of the AP2 μ2 subunit alone vary between 10 ...
Sorry about my previous reply. The question was for DNA sequence motifs and my answer was for protein sequence motifs. The TFD database has several DNA sequence motifs found in yeast, however it is a Transcription Factor Database and would lack some of the types of sequence motifs that the original message was requesting. TFD is available as flat files, in a variety of formats, via anonymous ftp from ncbi.nlm.nih.gov look in the repository/TFD directory. TFD is the creation of D. Ghosh, NCBI. Mike ...
Previous studies have identified a number of mutants and/or motifs that affect ASIC channel trafficking and/or function [28-34]. Most of these studies focused on ASIC1a. Our results demonstrated that the LL motifs in ASIC2a are important for its trafficking and function. All the mutants that we studied here had increased surface level (Fig. 1). However, only the DAA mutant exhibited a significant increase in surface:total ratio while the AADAA mutant had a marginal effect (p = 0.049). These data, together with our current recordings, indicate that most of the effect on ASIC2a surface trafficking and channel function was mainly mediated by the second LL motif. We speculate that the exact location of the LL motif may contribute to the differences observed between mutating the two LL motifs. It remains unclear as to the exact mechanism of how the LL motifs regulate ASIC2a. Our data here showed that the AADAA and DAA mutants increased the maturation of N-linked glycans. N-glycosylation is an ...
TY - JOUR. T1 - Extracting Best Consensus Motifs from Positive and Negative Examples. AU - Tateishi, Erika. AU - Maruyama, Osamu. AU - Miyano, Satoru. PY - 1995/10/27. Y1 - 1995/10/27. N2 - We define the best consensus motif (BCM) problem motivated by the problem of extracting motifs from nucleic acid and amino acid sequences. A type over an alphabetΣ is a familyΩ of subsets of Σ. A motif π of type Ω is a stringπ=π_1…π_n of motif components, each of which stands for an element in Ω. The BCM problem for Ω is, given a yes-no sample S={(α^,(1),, β^,(1),),...,(α^,(m),, β^,(m),)} of pairs of strings inΣ with α^,(i),≠β^,(i), for 1≤i≤m, to find a motif π of type Ω that maximizes the number of good pairs in S, where (α^,(i),,β^,(i),) is good forπ if π accepts α^,(i), and rejects β^,(i),. We prove that the BCM problem is NP-complete even for a very simple type Ω_1={z,φ≠z⊆Σ}, which is used, in practice, for describing protein motifs in the PROSITE database. We also ...
Shop RNA-binding motif protein ELISA Kit, Recombinant Protein and RNA-binding motif protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
The cell-extrinsic apoptotic pathway triggers programmed cell death in response to certain ligands that bind to cell-surface death receptors. Apoptosis is essential for normal development and homeostasis in metazoans, and furthermore, selective activation of the cell-extrinsic pathway in tumor cells holds considerable promise for cancer therapy. We used phage display to identify peptides and synthetic antibodies that specifically bind to the human proapoptotic death receptor DR5. Despite great differences in overall size and structure, the DR5-binding peptides and antibodies shared a tripeptide motif, which was conserved within a disulfide-constrained loop of the peptides and the third complementarity determining region of the antibody heavy chains. The X-ray crystal structure of an antibody in complex with DR5 revealed that the tripeptide motif is buried at the core of the interface, confirming its central role in antigen recognition. We found that certain peptides and antibodies exhibited ...
One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of related data elements. With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation. Herein, we present a structured syntax of minimotifs and their functional annotation. A syntax-based model of minimotif function with established
C. elegans NAB-1 protein; contains similarity to Pfam domains PF07647 (SAM domain (Sterile alpha motif)), PF00595 (PDZ domain (Also known as DHR or GLGF)), PF00536 (SAM domain (Sterile alpha motif))contains similarity to Interpro domains IPR001660 (Sterile alpha motif SAM), IPR001478 (PDZ/DHR/GLGF ...
Activity of SRs is not only regulated by ligand binding but also by interacting cofactors. The best-described binding site for SR coregulators is the hydrophobic cleft in the LBD to which LxxLL motifs can bind. The AR LBD is unique in its preference for the interaction with cofactors carrying FxxLF motifs rather than LxxLL motifs (Dubbink et al., 2004; Hur et al., 2004). The AR itself also contains an FQNLF motif in the N-terminal domain, enabling interaction with the LBD (N/C interaction; Doesburg et al., 1997; He et al., 2000). The potential competition between the AR N-terminal FQNLF motif and similar motifs in cofactors for interaction with the LBD raises questions regarding the role of the N/C interaction in orchestrating cofactor interactions. To study AR N/C interactions in living cells, we tagged the AR at the N and C termini with YFP and CFP, respectively, or with CFP alone, and applied FRET and simultaneous FRET and FRAP experiments. In addition, to investigate cofactor interactions, ...
Background Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions. Methodology/Principal Findings Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have a related cellular or molecular function, the prediction is more likely to be accurate. This filter was implemented in Minimotif Miner using function annotations from the Gene Ontology. We have also combined two filters that are based on entirely different principles and this combined filter has a better
Offers an approach for motif discovery based on a Bayesian approach. BAMM!motif is an application that exploits Bayesian Markov Models (BaMMs) to perform its predictions. It consists of four distinct modules allowing users to: (i) investigate nucleotide sequence to determine high-order motifs; (ii) explore model repositories with a feature for searching given motifs against a pre-computed database; and (iii) detect motifs occurrences from sequences.
PTMs (posttranslational modifications) such as ubiquitylation, sumoylation, acetylation and protein methylation are pivotal modifiers that determine the activation, deactivation or subcellular localization of signaling proteins, facilitating the initiation, amplification and transduction of signaling. Accumulating evidence suggest that several key signaling molecules in Hippo signaling pathway are tightly regulated by various types of PTMs. Malfunction of these critical signaling modules such as YAP/TAZ, MAT1/2 and LATS1/2 due to deregulated PTMs has been linked to a variety of human diseases such as cancer. In this review article, we summarized the current understanding of the impact of PTMs in regulating Hippo signaling pathway and further discussed the potential therapeutic intervention from the view of PTMs and Hippo pathway.
May play a role in the process of differentiation and maturation of neuronal cells (By similarity). May regulate the activity of TRIM17 (By similarity). Is a negative regulator of PAX6 expression (By similarity).
Bacterial surfaces are complex, built of from membranes, peptide-glycans and, importantly, proteins. The proteins play crucial roles as the key regulator of how the bacterium interacts with its environment. A full catalog of the motifs in coiled-coil proteins and their relative conservation grade is a pre-requisite to target the protein-protein interaction that bacterial surface protein makes to host proteins. Here, we present a greedy approach to iteratively identify conserved motifs in large sequence collections, identify all occurrences of these motifs and mask them. Remaining unmasked sequences are subjected to the second round of motif detection until no more significant motifs can be found or all protein segments have been assigned to a motif. We present the results for the S. pyogenes M protein. Given the speed and flexibility of our approach, we believe it will be useful in breaking analyzing surface protein of pathogens as these proteins are under high selective pressure and therefore cannot be
This gene was identified by involvement in some t(X;14) translocations associated with mature T-cell proliferations. This region has a complex gene structure, with a common promoter and 5 exon spliced to two different sets of 3 exons that encode two different proteins. This gene represents the downstream 8 kDa protein that localizes to mitochondria.[provided by RefSeq, Mar 2009 ...
Ret finger proteinRING finger protein 76, RFPtripartite motif protein TRIM27, RNF76RFP transforming protein, Tripartite motif-containing protein 27, tripartite motif-containing 27, tripartite motif containing 27, zinc finger protein ...
Accuracy. If you search with a simple motif, you can adjust the accuracy of the motif to the match on the sequence. If you type in a simple motif and let the accuracy be 80%, the motif search algorithm runs through the input sequence and finds all subsequences of the same length as the simple motif such that the fraction of identity between the subsequence and the simple motif is at least 80%. A motif match is added to the sequence as an annotation with the exact fraction of identity between the subsequence and the simple motif. If you use a list of motifs, the accuracy applies only to the simple motifs in the list ...
One focus of our research is to further our understanding of the physico-chemical properties of non-canonical nucleic acid structures. In this work, DNA hairpins are used to mimic a common motif present in RNA, i.e., a stem-loop motif with a bulge or inte
Ji, H. H., & Ostap, E. M. (2020). The regulatory protein 14-3-3β binds to the IQ motifs of myosin-IC independent of phosphorylation. Journal of Biological Chemistry, 295(12), 3749-3756. https://doi.org/10.1074/jbc. ...
C. elegans ETR-1 protein; contains similarity to Pfam domain PF00076 (RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain))contains similarity to Interpro domains IPR012677 (Nucleotide-binding, alpha-beta plait), IPR000504 (RNA-binding region RNP-1 (RNA recognition motif ...
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TRIM37 (tripartite motif-containing 37), Authors: Elif Ayse Erson,.M Elizabeth Petty. Published in: Atlas Genet Cytogenet Oncol Haematol.
Evidence 3: Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pr: putative ...
Evidence 3: Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pt: putative ...
UHMK1 (U2AF homology motif kinase 1), Authors: Vanessa Cristina Arfelli, Leticia Fröhlich Archangelo. Published in: Atlas Genet Cytogenet Oncol Haematol.
Active Motif offers a variety of ChIP Accessory Products that make it even easier to perform successful ChIP when working with our ChIP-IT Express Kitsand our Specialized ChIP-IT Kits.
Active Motif offers research kits, assays and biocomputing systems that help researchers study the function, regulation and interactions between genes, proteins and metabolic pathways.
Active Motif offers research kits, assays and biocomputing systems that help researchers study the function, regulation and interactions between genes, proteins and metabolic pathways.
Motif Bio Plc (LON:MTFB) CEO Dr Graham Lumsden talks to DirectorsTalk about the dosing of the first patient in the iclaprim Phase 3 trials to treat skin in
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