Amino Acid Motifs
Amino Acid Sequence
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Sequence Homology, Amino Acid
Amino Acids
Base Sequence
Conserved Sequence
Cloning, Molecular
Sequence Alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Binding Sites
Mutagenesis, Site-Directed
Amino Acid Substitution
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Protein Binding
Recombinant Fusion Proteins
DNA, Complementary
Mutation
Structure-Activity Relationship
Escherichia coli
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Models, Molecular
Protein Conformation
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
DNA Primers
Sequence Analysis, DNA
Peptide Fragments
Sequence Homology, Nucleic Acid
Consensus Sequence
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
Peptides
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Multigene Family
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Plasmids
Transfection
Amino Acids, Essential
Protein Structure, Secondary
Plant Proteins
Mutagenesis
Carrier Proteins
Substrate Specificity
Membrane Proteins
Amino Acid Transport Systems
DNA-Binding Proteins
Open Reading Frames
Sequence Analysis, Protein
RNA, Messenger
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Complementarity Determining Regions
Three regions (CDR1; CDR2 and CDR3) of amino acid sequence in the IMMUNOGLOBULIN VARIABLE REGION that are highly divergent. Together the CDRs from the light and heavy immunoglobulin chains form a surface that is complementary to the antigen. These regions are also present in other members of the immunoglobulin superfamily, for example, T-cell receptors (RECEPTORS, ANTIGEN, T-CELL).
COS Cells
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
Transcription Factors
Saccharomyces cerevisiae
Species Specificity
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Electrophoresis, Polyacrylamide Gel
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Transcription, Genetic
Cercopithecus aethiops
Evolution, Molecular
Cell Membrane
Protein Processing, Post-Translational
Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.
Restriction Mapping
Nucleotide Motifs
HeLa Cells
Receptors, Antigen, T-Cell, alpha-beta
Nuclear Proteins
Cells, Cultured
Aspartic Acid
Arabidopsis
Proteins
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Signal Transduction
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
Protein Sorting Signals
Clone Cells
A group of genetically identical cells all descended from a single common ancestral cell by mitosis in eukaryotes or by binary fission in prokaryotes. Clone cells also include populations of recombinant DNA molecules all carrying the same inserted sequence. (From King & Stansfield, Dictionary of Genetics, 4th ed)
Alanine
Cricetinae
Isoleucine
Amino Acid Transport Systems, Basic
Chromatography, High Pressure Liquid
Point Mutation
Codon
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Glycine
Cattle
Cytoplasm
Proline
Biological Transport
Gene Library
Protein Biosynthesis
Trypsin
Genes
Glutamine
Protein Interaction Domains and Motifs
Cyanogen Bromide
Valine
Phenylalanine
Gene Expression
Repetitive Sequences, Amino Acid
Excitatory Amino Acids
Blotting, Northern
Nitrogen
Promoter Regions, Genetic
Tryptophan
An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.
Macromolecular Substances
Sequence Analysis
Amino Acid Transport System A
Threonine
Serine
Helix-Turn-Helix Motifs
The first DNA-binding protein motif to be recognized. Helix-turn-helix motifs were originally identified in bacterial proteins but have since been found in hundreds of DNA-BINDING PROTEINS from both eukaryotes and prokaryotes. They are constructed from two alpha helices connected by a short extended chain of amino acids, which constitute the "turn." The two helices are held at a fixed angle, primarily through interactions between the two helices. (From Alberts et al., Molecular Biology of the Cell, 3d ed, p408-9)
Crystallography, X-Ray
Oligodeoxyribonucleotides
Catalysis
Genetic Complementation Test
Phosphorylation
Rabbits
Saccharomyces cerevisiae Proteins
Chickens
Tyrosine
Endopeptidases
RNA
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Dimerization
Circular Dichroism
Chromosome Mapping
Liver
Chromatography, Gel
Swine
Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).
Gene Expression Regulation
Peptide Mapping
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
Receptors, Amino Acid
Cell surface proteins that bind amino acids and trigger changes which influence the behavior of cells. Glutamate receptors are the most common receptors for fast excitatory synaptic transmission in the vertebrate central nervous system, and GAMMA-AMINOBUTYRIC ACID and glycine receptors are the most common receptors for fast inhibition.
Exons
Catalytic Domain
Blotting, Southern
Temperature
Chymotrypsin
Chromatography, Ion Exchange
Dietary Proteins
Magnetic Resonance Spectroscopy
Mass Spectrometry
Computational Biology
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Glutamic Acid
Amino Acyl-tRNA Synthetases
Sequence Homology
Phenotype
Oligonucleotide Probes
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
CHO Cells
Aminoisobutyric Acids
Two-Hybrid System Techniques
Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
Protein Transport
Nucleic Acid Conformation
Mutation, Missense
Molecular Structure
Hydrogen-Ion Concentration
Serine Endopeptidases
Gene Expression Regulation, Bacterial
Tissue Distribution
Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
Asparagine
Models, Biological
Binding, Competitive
Repressor Proteins
Alternative Splicing
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
RNA-Binding Proteins
Cystine
Ligands
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Glycoproteins
Glycosylation
Carbon Isotopes
Plants
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
Isoenzymes
Algorithms
Large Neutral Amino Acid-Transporter 1
Huckebein repressor activity in Drosophila terminal patterning is mediated by Groucho. (1/11917)
The Groucho corepressor mediates negative transcriptional regulation in association with various DNA-binding proteins in diverse developmental contexts. We have previously implicated Groucho in Drosophila embryonic terminal patterning, showing that it is required to confine tailless and huckebein terminal gap gene expression to the pole regions of the embryo. Here we reveal an additional requirement for Groucho in this developmental process by establishing that Groucho mediates repressor activity of the Huckebein protein. Putative Huckebein target genes are derepressed in embryos lacking maternal groucho activity and biochemical experiments demonstrate that Huckebein physically interacts with Groucho. Using an in vivo repression assay, we identify a functional repressor domain in Huckebein that contains an FRPW tetrapeptide, similar to the WRPW Groucho-recruitment domain found in Hairy-related repressor proteins. Mutations in Huckebein's FRPW motif abolish Groucho binding and in vivo repression activity, indicating that binding of Groucho through the FRPW motif is required for the repressor function of Huckebein. Taken together with our earlier results, these findings show that Groucho-repression regulates sequential aspects of terminal patterning in Drosophila. (+info)Two di-leucine-based motifs account for the different subcellular localizations of the human endothelin-converting enzyme (ECE-1) isoforms. (2/11917)
Endothelin-converting enzyme (ECE-1) is a type II integral membrane protein which plays a key role in the biosynthetic pathway of the vasoconstricting endothelins. Three ECE-1 isoforms, differing by their N-terminal cytoplasmic tails, are generated from a single gene. When expressed in CHO cells, they display comparable enzymatic activity but whereas ECE-1a is strongly expressed at the cell surface, ECE-1b is exclusively intracellular and ECE-1c presents an intermediate distribution. In the present study these different localizations were further described at the ultrastructural level, by electron microscope immunocytochemistry. To characterize the motifs responsible for the intracellular localization of ECE-1b we constructed chimeric proteins and point mutants. Two di-leucine-based motifs, contained in the N-terminal part of ECE-1b, were thus identified. One of these motifs (LV), displayed by both ECE-1b and ECE-1c, accounts for the reduced surface expression of ECE-1c as compared to ECE-1a. Mutation of both motifs (LL and LV) induces a very strong appearance of ECE-1b at the cell surface indicating that their presence in the N-terminal extremity of ECE-1b is critical for its exclusively intracellular localization. (+info)An Arabidopsis cDNA encoding a DNA-binding protein that is highly similar to the DEAH family of RNA/DNA helicase genes. (3/11917)
A cDNA encoding a putative RNA and/or DNA helicase has been isolated from Arabidopsis thaliana cDNA libraries. The cloned cDNA is 5166 bases long, and its largest open reading frame encodes 1538 amino acids. The central region of the predicted protein is homologous to a group of nucleic acid helicases from the DEAD/H family. However, the N- and C-terminal regions of the Arabidopsis cDNA product are distinct from these animal DEIH proteins. We have found that the C-terminal region contains three characteristic sequences: (i) two DNA-binding segments that form a probe helix (PH) involved in DNA recognition; (ii) an SV40-type nuclear localization signal; and (iii) 11 novel tandem-repeat sequences each consisting of about 28 amino acids. We have designated this cDNA as NIH (nuclear DEIH-boxhelicase). Functional character-ization of a recombinant fusion product containing the repeated region indicates that NIH may form homodimers, and that this is the active form in solution. Based on this information and the observation that the sequence homology is limited to the DEAH regions, we conclude that the biological roles of the plant helicase NIH differ from those of the animal DEIH family. (+info)A conserved motif N-terminal to the DNA-binding domains of myogenic bHLH transcription factors mediates cooperative DNA binding with pbx-Meis1/Prep1. (4/11917)
The t(1;19) chromosomal translocation of pediatric pre-B cell leukemia produces chimeric oncoprotein E2a-Pbx1, which contains the N-terminal transactivation domain of the basic helix-loop-helix (bHLH) transcription factor, E2a, joined to the majority of the homeodomain protein, Pbx1. There are three Pbx family members, which bind DNA as heterodimers with both broadly expressed Meis/Prep1 homeo-domain proteins and specifically expressed Hox homeodomain proteins. These Pbx heterodimers can augment the function of transcriptional activators bound to adjacent elements. In heterodimers, a conserved tryptophan motif in Hox proteins binds a pocket on the surface of the Pbx homeodomain, while Meis/Prep1 proteins bind an N-terminal Pbx domain, raising the possibility that the tryptophan-interaction pocket of the Pbx component of a Pbx-Meis/Prep1 complex is still available to bind trypto-phan motifs of other transcription factors bound to flanking elements. Here, we report that Pbx-Meis1/Prep1 binds DNA cooperatively with heterodimers of E2a and MyoD, myogenin, Mrf-4 or Myf-5. As with Hox proteins, a highly conserved tryptophan motif N-terminal to the DNA-binding domains of each myogenic bHLH family protein is required for cooperative DNA binding with Pbx-Meis1/Prep1. In vivo, MyoD requires this tryptophan motif to evoke chromatin remodeling in the Myogenin promoter and to activate Myogenin transcription. Pbx-Meis/Prep1 complexes, therefore, have the potential to cooperate with the myogenic bHLH proteins in regulating gene transcription. (+info)Drosophila and human RecQ5 exist in different isoforms generated by alternative splicing. (5/11917)
Members of the RecQ helicase superfamily have been implicated in DNA repair, recombination and replication. Although the genome of the budding yeast Saccharomyces cerevisiae encodes only a single member of this family, there are at least five human RecQ-related genes: RecQL, BLM, WRN, RecQ4 and RecQ5. Mutations in at least three of these are associated with diseases involving a predisposition to malignancies and a cellular phenotype that includes increased chromosome instability. Metazoan RecQ helicases are defined by a core region with characteristic helicase motifs and sequence similarity to Escherichia coli RecQ protein. This core region is typically flanked by extensive, highly charged regions, of largely unknown function. The recently reported human RecQ5, however, has only the core RecQ-homologous region. We describe here the identification of the Drosophila RecQ5 gene. We recovered cDNAs corresponding to three alternative splice forms of the RecQ5 transcript. Two of these generate nearly identical 54 kDa proteins that, like human RecQ5, consist of the helicase core only. The third splice variant encodes a 121 kDa isoform that, like other family members, has a C-terminal extension rich in charged residues. A combination of RACE and cDNA analysis of human RECQ5 demonstrates extensive alternative splicing for this gene also, including some forms lacking helicase motifs and other conserved regions. (+info)The acidic domain and first immunoglobulin-like loop of fibroblast growth factor receptor 2 modulate downstream signaling through glycosaminoglycan modification. (6/11917)
Fibroblast growth factor receptors (FGFRs) are membrane-spanning tyrosine kinases that have been implicated in a variety of biological processes including mitogenesis, cell migration, development, and differentiation. We identified a unique isoform of FGFR2 expressed as a diffuse band with an unusually large molecular mass. This receptor is modified by glycosaminoglycan at a Ser residue located immediately N terminal to the acidic box, a stretch of acidic amino acids. The acidic box and the glycosaminoglycan modification site are encoded by an alternative exon of the FGFR2 gene. The acidic box appears to play an important role in glycosaminoglycan modification, and the presence of this domain is required for modification by heparan sulfate glycosaminoglycan. Moreover, the presence of the first immunoglobulin-like domain encoded by another alternative exon abrogated the modification. The high-affinity receptor with heparan sulfate modification enhanced receptor autophosphorylation, substrate phosphorylation, and ternary complex factor-independent gene expression. It also sustained mitogen-activated protein kinase activity and increased eventual DNA synthesis, a long-term response to fibroblast growth factor stimulation, at physiological ligand concentrations. We propose a novel regulation mechanism of FGFR2 signal transduction through glycosaminoglycan modification. (+info)The net repressor is regulated by nuclear export in response to anisomycin, UV, and heat shock. (7/11917)
The ternary complex factors (TCFs) are targets for Ras/mitogen-activated protein kinase signalling pathways. They integrate the transcriptional response at the level of serum response elements in early-response genes, such as the c-fos proto-oncogene. An important aim is to understand the individual roles played by the three TCFs, Net, Elk1, and Sap1a. Net, in contrast to Elk1 and Sap1a, is a strong repressor of transcription. We now show that Net is regulated by nuclear-cytoplasmic shuttling in response to specific signalling pathways. Net is mainly nuclear under both normal and basal serum conditions. Net contains two nuclear localization signals (NLSs); one is located in the Ets domain, and the other corresponds to the D box. Net also has a nuclear export signal (NES) in the conserved Ets DNA binding domain. Net is apparently unique among Ets proteins in that a particular leucine in helix 1, a structural element, generates a NES. Anisomycin, UV, and heat shock induce active nuclear exclusion of Net through a pathway that involves c-Jun N-terminal kinase kinase and is inhibited by leptomycin B. Nuclear exclusion relieves transcriptional repression by Net. The specific induction of nuclear exclusion of Net by particular signalling pathways shows that nuclear-cytoplasmic transport of transcription factors can add to the specificity of the response to signalling cascades. (+info)Regulation of RelA subcellular localization by a putative nuclear export signal and p50. (8/11917)
Nuclear factor kappaB (NF-kappaB) represents a family of dimeric DNA binding proteins, the pleotropic form of which is a heterodimer composed of RelA and p50 subunits. The biological activity of NF-kappaB is controlled through its subcellular localization. Inactive NF-kappaB is sequestered in the cytoplasm by physical interaction with an inhibitor, IkappaBalpha. Signal-mediated IkappaBalpha degradation triggers the release and subsequent nuclear translocation of NF-kappaB. It remains unknown whether the NF-kappaB shuttling between the cytoplasm and nucleus is subjected to additional steps of regulation. In this study, we demonstrated that the RelA subunit of NF-kappaB exhibits strong cytoplasmic localization activity even in the absence of IkappaBalpha inhibition. The cytoplasmic distribution of RelA is largely mediated by a leucine-rich sequence homologous to the recently characterized nuclear export signal (NES). This putative NES is both required and sufficient to mediate cytoplasmic localization of RelA as well as that of heterologous proteins. Furthermore, the cytoplasmic distribution of RelA is sensitive to a nuclear export inhibitor, leptomycin B, suggesting that RelA undergoes continuous nuclear export. Interestingly, expression of p50 prevents the cytoplasmic expression of RelA, leading to the nuclear accumulation of both RelA and p50. Together, these results suggest that the nuclear and cytoplasmic shuttling of RelA is regulated by both an intrinsic NES-like sequence and the p50 subunit of NF-kappaB. (+info)
A C-terminal motif targets hedgehog to axons, coordinating assembly of the Drosophila eye and brain | Kunes Laboratory
ELM: the status of the 2010 eukaryotic linear motif resource
Design and evaluation of antimalarial peptides derived from prediction of short linear motifs in proteins related to...
Edwards Lab: SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent
SLiMSuite & SeqSuite: open-source bioinformatics in Python: May 2012
Leucine-rich PPR motif-containing protein elisa and antibody
Reactome | SMAD2/3 Phosphorylation Motif Mutants in Cancer
The structural basis of SMS (Short Motif Sequence) - mediated communication between proteins: characterization, modeling and...
question about motif enrichment analysis using PWMenrich
IJMS | Free Full-Text | Recurrent Structural Motifs in Non-Homologous Protein Structures | HTML
The eukaryotic linear motif resource ELM: 10 years and counting
Edwards Lab: 2010
An evolutionary and functional assessment of regulatory network motifs | Genome Biology | Full Text
PRINTS Search
Tripartite motif-containing protein 42
Inspired by the main element role of super-helical motifs in molecular - Plk1 Inhibitor BI-2536 suppresses cell growth and...
mouse Slo2 protein
Summary Report | CureHunter
Short Match Track Settings
Short Match Track Settings
Short Match Track Settings
A general procedure for locating and analyzing protein-binding sequence motifs in nucleic acids | PNAS
PRINTS Search
Vonderheide, RH]
Trim21 MGI Mouse Gene Detail - MGI:106657 - tripartite motif-containing 21
Trim33 MGI Mouse Gene Detail - MGI:2137357 - tripartite motif-containing 33
Feature map marking the locations of 4G-, 3G- and 2G-co | Open-i
DiffLogo : a comparative visualization of sequence motifs | BMC Bioinformatics | Full Text
Two motifs target Batten disease protein CLN3 to lysosomes in transfected nonneuronal and neuronal cells. - NextBio article
Structural motif - Wikipedia
SMART: ChSh domain annotation
Red Hat Motif 2.1 now shipping
Cytoplasmic short linear motifs in ACE2 and integrin β3 link SARS-CoV-2 host cell receptors to mediators of endocytosis and...
DNA consensus seqs
Two di-leucine motifs regulate trafficking and function of mouse ASIC2a | Molecular Brain | Full Text
Extracting Best Consensus Motifs from Positive and Negative Examples<...
RNA-binding motif protein elisa and antibody
2h9g - Proteopedia, life in 3D
A proposed syntax for Minimotif Semantics, version 1 | BMC Genomics | Full Text
RNAiDB Tree View
Compartmentalization of androgen receptor protein-protein interactions in living cells | JCB
Partitioning of Minimotifs Based on Function with Improved Prediction by Sanguthevar Rajasekaran, Tian Mi et al.
BaMM!motif - omicX
New insights into posttranslational modifications of Hippo pathway in carcinogenesis and therapeutics | Cell Division | Full...
Trim44 - Tripartite motif-containing protein 44 - Rattus norvegicus (Rat) - Trim44 gene & protein
Greedy motif-based approach to parsing large and diverge coiled-coil proteins into domains [PeerJ Preprints]
Cx9C motif-containing protein 4
TRIM27 Antibody | scrazzl.com - Simply Connecting Science
QIAGEN Bioinformatics Manuals
PPC Measurements of Unfolding Volumes of DNA Stem-Loop Motifs
Ji, H. H., & Ostap, E. M. (2020). The regulatory protein 14-3-3β binds to the IQ motifs of myosin-IC independent of...
RNAiDB Tree View
The p53 cofactor Strap exhibits an unexpected TPR motif and oligonucleotide-binding (OB)-fold structure - Nuffield Department...
Active Motif » Active Motif careers
TRIM37 (tripartite motif-containing 37)
B. subtilis Expression Data Browser
B. subtilis Expression Data Browser
UHMK1 (U2AF homology motif kinase 1)
Active Motif » ChIP Accessory Products for more successful chromatin IP
Active Motif » Recombinant ErbB-2 protein
Active Motif » Recombinant PDGFRb protein
Motif Bio Plc CEO Dr Graham Lumsden Interview: First Patient dosed
Skirt with jacquard plaid motif | Woman | Emporio Armani
NEROLI Luxus Parfüméria
BAHD acyltransferase
Members of this enzyme family typically share two conserved amino acid motifs. The first motif, or string of consecutive amino ... The second conserved motif is DFGWG (Aspartic acid, Phenylalanine, Glycine, Tryptophan, Glycine) and it is typically found near ... Phylogenetic analysis using full-length amino acid sequences of functionally characterized BAHD enzymes by D'Auria (2006) and ... Aspartic acid) and it is typically found in the central region of the protein. The Histidine in this motif has also been shown ...
Calmodulin 1
Calmodulin contains 148 amino acids and has 4 calcium-binding EF hand motifs. Its functions include roles in growth and the ... Li Z, Sacks DB (Feb 2003). "Elucidation of the interaction of calmodulin with the IQ motifs of IQGAP1". J. Biol. Chem. 278 (6 ...
Pentatricopeptide repeat
The pentatricopeptide repeat (PPR) is a 35-amino acid sequence motif. Pentatricopeptide-repeat-containing proteins are a family ... They are distinguished by the presence of tandem degenerate PPR motifs and by the relative lack of introns in the genes coding ...
Glycine receptor
... identification of amino acid sequence motifs governing subunit stoichiometry". Neuron. 11 (6): 1049-56. doi:10.1016/0896-6273( ... The receptor can be activated by a range of simple amino acids including glycine, β-alanine and taurine, and can be selectively ... The glycine receptor (abbreviated as GlyR or GLR) is the receptor of the amino acid neurotransmitter glycine. GlyR is an ...
Gluten immunochemistry
McLachlan A, Cullis PG, Cornell HJ (October 2002). "The use of extended amino acid motifs for focussing on toxic peptides in ... The IRP lies within a 25 amino-acid long region that is resistant to pancreatic proteases. The 25mer is also resistant to Brush ... HLA-DQ proteins present polypeptide regions of proteins of about 9 amino acids and larger in size (10 to 14 residues in ... Α2-gliadin differs from the other α-gliadins, specifically because it contains an insert of 14 amino acids. This particular ...
Fig4
The Sac1 phosphatase domain encompasses approximately 400 amino acids and consists of seven conserved motifs. It harbors the ... In humans, the FIG4 gene localizes on chromosome 6 and encodes a Sac3 protein of 907 amino acids. Sac3 is characterized as a ...
Cordon-bleu protein
The WH2 domain is an ~18-21 amino acids actin-binding motif. This domain was first recognized as an essential element for the ... The human COBL gene encodes a 1261-amino acid protein with a mass of about 136 kDa. The mouse protein is 1337 amino acids long ... Cobl Homology domains contain three motifs following the consensus KrRAPpPP (first described as "KRAP" motif of unknown ... The WH2 motif in WASp recruits ATP-G-actin that binds to either Arp2 or Arp3 to complete the formation of a trimeric actin ...
RAB2B
It has a motif domain between the amino acids 35 and 43. Due to the alternative splicing, two isoforms of this same protein ... Isoform 2 consists just of 151 amino acids, having a mass of 16,667 Da. Small GTPases of the RAB superfamily are recognized as ... Even though these RAB family proteins are highly homologous to each other (RAB2A and RAB2B have 85.8% amino acid identity), the ...
Armadillo repeat
Peifer M, Berg S, Reynolds AB (1994). "A repeating amino acid motif shared by proteins with diverse cellular roles". Cell. 76 ( ... Eukaryotic Linear Motif resource motif class TRG_NLS_Bipartite_1 Eukaryotic Linear Motif resource motif class TRG_NLS_MonoCore_ ... 2 Eukaryotic Linear Motif resource motif class TRG_NLS_MonoExtC_3 Eukaryotic Linear Motif resource motif class TRG_NLS_MonoExtN ... An armadillo repeat is the name of a characteristic, repetitive amino acid sequence of about 40 residues in length that is ...
Beta-catenin
Peifer M, Berg S, Reynolds AB (March 1994). "A repeating amino acid motif shared by proteins with diverse cellular roles". Cell ... Liu J, Xing Y, Hinds TR, Zheng J, Xu W (June 2006). "The third 20 amino acid repeat is the tightest binding site of APC for ... First, they might reach or even surpass the length of 30 amino acids in length, and contact the ARM domain on an excessively ... There is one requirement, though: substrates of GSK3 need to be pre-phosphorylated four amino acids downstream (C-terminally) ...
Ornithine transcarbamylase
SMG stands for the conserved amino acid motif of Ser-Met-Gly. Upon closure, these residues interact with L-ornithine. The ... Orotic acid is a product of this pathway. Increased levels of orotic acid in urine can be an indicator that a patient is ... Postranscriptional modification leaves the mature peptide with 322 amino acids and a weight of 36.1 kD. The protein is located ... Anabolic OTC facilitates the sixth step in the biosynthesis of the amino acid arginine in prokaryotes. In contrast, mammalian ...
Cytokine receptor
... whose members have certain conserved motifs in their extracellular amino-acid domain. The IL-2 receptor belongs to this chain, ...
TGF alpha
The EGF receptor is characterized by having an extracellular domain that has numerous amino acid motifs. EGFR is essential for ... TGF-α is synthesized internally as part of a 160 (human) or 159 (rat) amino acid transmembrane precursor. The precursor is ... 50 amino acids of TGF-α, and a 35-residue-long cytoplasmic domain. In its smallest form, TGF-α has six cysteines linked ... TGF-α has been shown to inhibit gastric acid secretion. TGF-α can be produced in macrophages, brain cells, and keratinocytes. ...
SdrG C terminal protein domain
The C terminus contain a LPXTG sequence motif and hydrophobic amino acid segments attached to peptidoglycan. The C-terminal ... the wall-anchoring LPTXG motif, a hydrophobic transmembrane region and a cytoplasmic tail of positively charged amino acid ... SdrG stands for serine-aspartate dipeptide repeats, which as its name suggests, contains repeats of two amino acids, serine and ...
KIAA1211L
The KIAA1211L protein has one domain called the DUF4592 motif and spans amino acids 131-239. This domain is highly conserved ... Additionally, this location (amino acids 24-43) is positively charged, probably due to the high amount of lysine at this ... The amino acids conserved among all the KIAA1211L orthologs are depicted in the conceptual translation. The KIAA1211L gene is ... KIAA1211 is located on chromosome 4 and has 1233 amino acids. Its percent identity to KIAA1211L is 21%. The KIAA1211 has an ...
RNA-dependent RNA polymerase
The catalytic center is formed by several motifs containing a number of conserved amino acid residues. Eukaryotic RNA ... Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the aspartic acid residues of these motifs are implied in the ... Birnaviral RNA replicase is unique in that it lacks motif C (GDD) in the palm. Mononegaviral RdRP (PDB 5A22) has been ... This RNA-directed RNA polymerase possesses a number of short regions and motifs homologous to other RNA-directed RNA ...
Nucleoprotein
For example, RNP in snRNPs have an RNA-binding motif in its RNA-binding protein. Aromatic amino acid residues in this motif ... they provide a rough model of the structure which allows for predictions of the identity of significant amino acids and ... This nucleic acid binding is strengthened by electrostatic attraction between the positive lysine side chains and the negative ... Nucleoproteins are any proteins that are structurally associated with nucleic acids, either DNA or RNA. Typical nucleoproteins ...
UBA protein domain
UBA domains have a common sequence motif of approximately 45 amino acid residues. They fold into three-helix bundle structures ... Hofmann K, Bucher P (May 1996). "The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination ...
C19orf44
There is also a predicted sumoylation motif from amino acid 212 to 221. C19orf44 is predicted to be localized in the nucleus or ... The amino acid sequence for C19orf44 was found to be serine rich using tools on EMBL-EBI. Additionally, there is a domain of ... It contains 10 exons that code for a 657 amino acid protein. There are 7 splice variants that exist for C19orf44. C19orf44 is ... located from amino acid 474 to 641. C19orf44 has experimentally determined phosphorylation sites at the S114 and S213 positions ...
Cyclic di-GMP
These proteins have either an EAL or an HD-GYP amino acid motif. Processes that are known to be regulated by cyclic di-GMP, at ... These proteins typically have a characteristic GGDEF motif, which refers to a conserved sequence of five amino acids. ... Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid P. Ross Nature, 1987 Benach, J; Swaminathan ... "Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid". Nature. 325 (6101): 279-81. doi:10.1038/ ...
RGS18
This protein contains a conserved 120 amino acid motif called the RGS domain. The protein attenuates the signaling activity of ...
List of Protein subcellular localization prediction tools
... sequence motifs and amino acid composition". Bioinformatics. 22 (10): 1158-65. doi:10.1093/bioinformatics/btl002. PMID 16428265 ... predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices". Amino ... Du P, Cao S, Li Y (November 2009). "SubChlo: predicting protein subchloroplast locations with pseudo-amino acid composition and ... Tusnády, Gábor E.; Simon, István (Oct 1998). "Principles governing amino acid composition of integral membrane proteins: ...
LRRN3
They are common in protein-protein interaction motifs and are typically 20-29 amino acids in length. All major classes of LRRs ... The LRRN3 protein is 708 amino acids in length. The molecular weight of this protein is 79,424 Daltons, with an isoelectric ... Leucine-rich repeats are unusually rich in the hydrophobic amino acid leucine. ...
Ptc1
This recruitment takes place via a 4 amino acid motif in the Ste5 phosphosites. Ptc1 is also involved in regulating the osmotic ...
C16orf46
A coronavirus cleavage site is predicted at the 235 amino acid position. There are also tyrosine motif locations between amino ... The full C16orf46 protein is 417 amino acids long. It has no isoforms, and its most distant ortholog, Rhincodon typus (whale ... acids 42-45 and 251-252. mRNA folding on the 5' UTR predicts a stem loop twice in the area between base pairs 47-90. C16orf46 ...
Discovery and development of integrase inhibitors
These amino acids form the DDE motif that coordinate divalent metal ions (Mg2+ or Mn2+). These metal ions are essential for the ... A loop containing amino acid residues 140-149 is located in the catalytic-core domain and is important for IN function as ... 2. The catalytic core domain (CCD), which encompasses amino acids 51- 212, contains the active site of IN but it can't catalyze ... 3. The C-terminal domain (CTD), which encompasses amino acids 213-288, binds DNA nonspecifically and its interaction with NTD ...
W-box
As predicted amino acids in the conserved WRKYGQK signature motif contact the W-box DNA. WRKY Transcription Factor Family at ... The W box is a deoxyribonucleic acid (DNA) cis-regulatory element sequence, (T)TGAC(C/T), which is recognized by the family of ... Nucleic Acids Research. 41 (21): 9764-9778. doi:10.1093/nar/gkt732. PMC 3834811. PMID 23975197. Yamasaki, K.; Kigawa T; ...
Endoplasmic reticulum
This motif is composed of four amino acids at the end of the protein sequence. The most common retention sequences are KDEL for ... The N-terminus (one end) of a polypeptide chain (i.e., a protein) contains a few amino acids that work as an address tag, which ... The first 5-30 amino acids polymerized encode a signal peptide, a molecular message that is recognized and bound by a signal ... either secreted constitutively with no tag or secreted in a regulatory manner involving clathrin and paired basic amino acids ...
Φ29 DNA polymerase
Bernad A, Blanco L, Salas M (September 1990). "Site-directed mutagenesis of the YCDTDS amino acid motif of the phi 29 DNA ... Involvement of two amino acid residues highly conserved in proofreading DNA polymerases". EMBO J. 15 (5): 1182-92. doi:10.1002/ ... His61 and Phe69 of the highly conserved ExoII motif are essential for interaction with the terminal protein". Nucleic Acids Res ... Truniger V, Blanco L, Salas M (1999). "Role of the "YxGG/A" motif of Phi29 DNA polymerase in protein-primed replication". J Mol ...
FANCG
The putative 622-amino acid protein has a leucine-zipper motif at its N-terminus. Fanconi anemia is an autosomal recessive ... Blom E, van de Vrugt HJ, de Vries Y, de Winter JP, Arwert F, Joenje H (January 2004). "Multiple TPR motifs characterize the ...
Chloroplast DNA
... rich in hydroxylated amino acids such as serine, threonine, and proline, and poor in acidic amino acids like aspartic acid and ... "Functional characterization of sequence motifs in the transit peptide of Arabidopsis small subunit of rubisco". Plant ... Chloroplast transit peptides exhibit huge variation in length and amino acid sequence.[42] They can be from 20-150 amino acids ... Tic100 is a nuclear encoded protein that's 871 amino acids long. The 871 amino acids collectively weigh slightly less than 100 ...
Bioinformática, a enciclopedia libre
Needleman, S. y Wunsch, C. (1970). "A general method applicable to the search for similarities in the amino acid sequence of ... "PRINTS-a protein motif fingerprint database". Protein Engineering 7 (7). ISSN 1741-0134, Páxs. 841-848. ... "Similar amino acid sequences: chance or common ancestry?". Science 214 (4517).. ... "Nucleic Acids Research 22 (17).. *↑ Un bo recurso de introdución a EMBnet é a páxina What is EMBnet? Arquivado 07 de setembro ...
RAD51
In humans, RAD51 is a 339-amino acid protein that plays a major role in homologous recombination of DNA during double strand ... Wong AK, Pero R, Ormonde PA, Tavtigian SV, Bartel PL (Dec 1997). "RAD51 interacts with the evolutionarily conserved BRC motifs ... They each share about 25% amino acid sequence identity with RAD51 and with each other.[28] ... "Nucleic Acids Research. 25 (19): 3868-74. doi:10.1093/nar/25.19.3868. PMC 146972 . PMID 9380510.. ...
TATA box
Four hydrogen bonds form between polar side chains on TBP amino acid (Asn27, Asn117, Thr82, Thr173)( and bases in the minor ... One study found less than 30% of 1031 potential promoter regions contain a putative TATA box motif in humans.[9] In Drosophila, ... "Nucleic Acids Research. 9 (19): 5145-58. doi:10.1093/nar/9.19.5145. PMC 327505. PMID 6171774.. ... The TATA box was the first eukaryotic core promoter motif to be identified in 1978 by American biochemist David Hogness[1] ...
Histone
The single-letter amino acid abbreviation (e.g., K for Lysine) and the amino acid position in the protein ... motif (DNA-binding protein motif that recognize specific DNA sequence). They also share the feature of long 'tails' on one end ... compared amino acid compositions in the same histone from different organisms, and compared amino acid sequences of the same ... 3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone". The Journal of ...
فهرست یهودیان برنده جایزه نوبل - ویکیپدیا، دانشنامهٔ آزاد
"for his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active ... "for his profoundly characteristic narrative art with motifs from the life of the Jewish people"[۵] ... "for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA"[۲۹] ... "for their contributions concerning the determination of base sequences in nucleic acids"[۲۹] ...
Pu'er tea
The microbes are also responsible for metabolising the carbohydrates and amino acids present in the tea leaves.[15][16][17] ... The press forces the tea into a metal form that is occasionally decorated with a motif in sunken-relief. Due to its efficiency ... Wet pile fermented pu'er has higher levels of caffeine and much higher levels of gallic acid compared with traditionally aged ...
Superoxide dismutase
... as all ingested SOD is broken down into amino acids before being absorbed. However, ingestion of SOD bound to wheat proteins ... The Ni-hook contains the motif His-Cys-X-X-Pro-Cys-Gly-X-Tyr; it provides most of the interactions critical for metal binding ... and their active sites contain the same type and arrangement of amino acid side-chains. They are usually dimers, but ... superoxide inactivates the citric acid cycle enzyme aconitase, can poison energy metabolism, and releases potentially toxic ...
Proteasome
The ubiquitin protein itself is 76 amino acids long and was named due to its ubiquitous nature, as it has a highly conserved ... which contains a specific motif (i.e., HbYX motif). The ATPases C-termini bind into pockets in the top of the 20S, and tether ... The mechanism for unfolding of globular proteins is necessarily general, but somewhat dependent on the amino acid sequence. ... The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into ...
LIG3, a enciclopedia libre
"Nucleic Acids Res. 28 (18): 3558-63. PMC 110727. PMID 10982876. doi:10.1093/nar/28.18.3558.. ... A iniciación da tradución alternativa e os mecanismos de empalme ou splicing alteran as secuencias amino- e carboxilo-terminais ... "DNA ligase III is recruited to DNA strand breaks by a zinc finger motif homologous to that of poly(ADP-ribose) polymerase. ... "Nucleic Acids Res. 23 (23): 4836-43. PMC 307472. PMID 8532526. doi:10.1093/nar/23.23.4836.. ...
Vitamin C
Mineral Nutrients and Amino Acids May or Must be Added.[87] Voluntary and mandatory fortification was described for various ... bind to a conserved Leu-Xaa-Xaa-Leu-Ala-Pro motif present in all substrates identified so far.. ... Ascorbic acid is a weak sugar acid structurally related to glucose. In biological systems, ascorbic acid can be found only at ... The biosynthesis of ascorbic acid in vertebrates starts with the formation of UDP-glucuronic acid. UDP-glucuronic acid is ...
Autophagy
In mammals, amino acid sensing and additional signals such as growth factors and reactive oxygen species regulate the activity ... The generated PtdIns(3)P is used as a docking point for proteins harboring a PtdIns(3)P binding motif. WIPI2, a PtdIns(3)P ... Z. Yang, J. Huang, J. Geng, U. Nair, and D. J. Klionsky, 'Atg22 Recycles Amino Acids to Link the Degradative and Recycling ... This allows unneeded proteins to be degraded and the amino acids recycled for the synthesis of proteins that are essential for ...
Tumor necrosis factor alpha
In an effort to localize the amino acid motif responsible for granule targeting, we constructed additional fusion proteins and ... TNF is primarily produced as a 233-amino acid-long type II transmembrane protein arranged in stable homotrimers.[24][25] From ... cellular response to amino acid stimulus. • negative regulation of extrinsic apoptotic signaling pathway in absence of ligand. ... The common house mouse TNFα and human TNF are structurally different.[28] The 17-kilodalton (kDa) TNF protomers (185-amino acid ...
Wiskott-Aldrich syndrome protein
The Wiskott-Aldrich Syndrome protein (WASp) is a 502-amino acid protein expressed in cells of the hematopoietic system. In the ... It is located towards the C-terminal end of the protein and contains four motifs: two verprolin homology motifs (VV) binds ... The presence of a number of different motifs suggests they are regulated by a number of different stimuli, and interact with ... and the acidic motif (A) binds Arp2/3.[8] In isolation, the VCA region is constitutively active. However, in full-length N-WASp ...
CCR5 - Википедија, слободна енциклопедија
Miyakawa T, Obaru K, Maeda K, Harada S, Mitsuya H (2002). „Identification of amino acid residues critical for LD78beta, a ... The BBXB motif of RANTES is the principal site for heparin binding and controls receptor selectivity". J. Biol. Chem. 276 (14 ... "Nucleic Acids Res. 18 (6): 1513-6. PMC 330519 . PMID 2183196. doi:10.1093/nar/18.6.1513.. CS1 одржавање: Експлицитна употреба ... Addition of ethanolamine-phosphoglycerol to specific glutamic acid residues on EF-1 alpha". J. Biol. Chem. 264 (24): 14334-41. ...
Cathelicidin
39-80 amino acid residues) are also present. These larger cathelicidins display repetitive proline motifs forming extended ... Cathelicidins range in size from 12 to 80 amino acid residues and have a wide range of structures.[8] Most cathelicidins are ... although amino acid residues thought to be important in such protease inhibition are usually lacking. ... linear peptides with 23-37 amino acid residues, and fold into amphipathic α-helices. Additionally cathelicidins may also be ...
CASS4
Isoform "a" of human CASS4 is considered the predominant species, and at 786 amino acids is the longest one.[10] Amino acid ... CAS proteins have an amino terminal SH3 domain enabling interaction with poly-proline motif-containing proteins such as FAK. ... 786 amino acids, considered the major isoform), the third one contains 6 exons and encodes a shorter isoform b (732 amino acids ... The CASS4 C-terminus has a short region of CAS family homology, but lacks obvious similarity at the level of primary amino acid ...
RTI-229
With the combination of two potent dopamine transporter (DAT) binding motifs attached to the tropane ring, the p-iodophenyl ... tropane-2 beta-carboxylic acid ester and amide analogues. New high-affinity and selective compounds for the dopamine ... 2-Amino-1,2-dihydronaphthalene. *2-Aminoindane. *5-(2-Aminopropyl)indole. *2-Aminotetralin ...
Aminoacyl tRNA synthetase
... beyond the twenty canonical amino acids found in nature, to include an unnatural amino acid as well. The unnatural amino acid ... Class I has two highly conserved sequence motifs. It aminoacylates at the 2'-OH of a terminal adenosine nucleotide on tRNA, and ... the tRNA with the amino acid. Once the tRNA is charged, a ribosome can transfer the amino acid from the tRNA onto a growing ... and redox-active amino acids.[14] Another use is introducing amino acids bearing reactive functional groups for chemically ...
Protein
Sequence motif. Short amino acid sequences within proteins often act as recognition sites for other proteins.[26] For instance ... The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino ... amino acids. All proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a ... If amino acids are present in the environment, microorganisms can conserve energy by taking up the amino acids from their ...
乙醯膽鹼酯酶 - 維基百科,自由的百科
Purification and partial amino acid sequence analysis of human erythrocyte acetylcholinesterase.. FEBS Lett. 1989, 247 (2): 279 ... 1vzj: STRUCTURE OF THE TETRAMERIZATION DOMAIN OF ACETYLCHOLINESTERASE: FOUR-FOLD INTERACTION OF A WWW MOTIF WITH A LEFT-HANDED ...
Hemoglobin
... are folded chains of a large number of different amino acids called polypeptides. The amino acid sequence of any polypeptide ... Such a name is given because this arrangement is the same folding motif used in other heme/globin proteins such as myoglobin.[ ... Variations in hemoglobin amino acid sequences, as with other proteins, may be adaptive. For example, hemoglobin has been found ... Hemoglobin has a quaternary structure characteristic of many multi-subunit globular proteins.[34] Most of the amino acids in ...
Cytochrome c
All cytochrome c proteins contain a characteristic CXXCH (cysteine-any-any-cysteine-histidine) amino acid motif that binds heme ... Its primary structure consists of a chain of about 100 amino acids. Many higher-order organisms possess a chain of 104 amino ... Its amino acid sequence is highly conserved in eukaryotes, differing by only a few residues. In more than thirty species, 34 of ... Amino acid sequences in cytochrome c proteins from different species, adapted from Strahler, Arthur; Science and Earth History ...
Mesa Verde National Park
The combination of corn and beans provided the Mesa Verdeans with the amino acids of a complete protein. When conditions were ... Common motifs in the rock art of the region include, anthropomorphic figures in procession and during copulation or childbirth ... patterns that resemble symbols used in pottery and zigzag that represent stitches used in basket making are common motifs. The ...
DLG1
"SAP97 is associated with the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor GluR1 subunit". The Journal of ... 97 to GluR-A alpha-amino-5-hydroxy-3-methyl-4-isoxazole propionate receptor subunit is determined by a novel sequence motif". ... "SAP97 is associated with the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor GluR1 subunit". The Journal of ... Bassand P, Bernard A, Rafiki A, Gayet D, Khrestchatisky M (Jun 1999). "Differential interaction of the tSXV motifs of the NR1 ...
Arachidonate 5-lipoxygenase
Human ALOX5 is a soluble, monomeric protein consisting of 673 amino acids with a molecular weight of ~78 kDa. Structurally, ... Variant alleles involved deletions (one or two) or additions (one, two, or three) of Sp1 motifs to the five tandem motifs ... Arachidonic acidEdit. ALOX5 metabolizes the omega-6 fatty acid, Arachidonic acid (AA, i.e. 5Z,8Z,11Z,15Z-eicosatrienoic acid), ... Eicosapentaenoic acidEdit. ALOX5 metabolizes the omega-3 fatty acid, Eicosapentaenoic acid (EPA, i.e. 4Z,8Z,11Z,14Z,17Z- ...
Serotonin-norepinephrine reuptake inhibitor
Serotonin is synthesized from an amino acid called L-tryptophan. Active transport system regulates the uptake of tryptophan ... The same motif can be found in reboxetine where it is constrained in a morpholine ring system. Some studies have been made ... This structural motif has potential for high affinity binding to biogenic amine transports.[28] Drugs containing an ...
p21
cellular response to amino acid starvation. • positive regulation of programmed cell death. • negative regulation of apoptotic ... Specifically it contains a Cy1 motif in the N-terminal half, and weaker Cy2 motif in the C-terminal domain that allow it to ... "Cyclin-binding motifs are essential for the function of p21CIP1". Molecular and Cellular Biology. 16 (9): 4673-4682. doi ...
Chemokine
... those with a specific amino acid sequence (or motif) of glutamic acid-leucine-arginine (or ELR for short) immediately before ... they share gene sequence and amino acid sequence homology. They all also possess conserved amino acids that are important for ... The CC chemokine (or β-chemokine) proteins have two adjacent cysteines (amino acids), near their amino terminus. There have ... A loop of approximately ten amino acids follows the first two cysteines and is known as the N-loop. This is followed by a ...
Muramyl ligase
... that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes ... 1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). ... N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence ...
Category:Amino acid motifs - Wikimedia Commons
Amino Acid Motifs (en); motifs dacides aminés (fr) Three-dimensional protein structural elements that are composed of a ... Amino Acid Motifs Three-dimensional protein structural elements that are composed of a combination of secondary structures. ... Media in category "Amino acid motifs". The following 52 files are in this category, out of 52 total. ... Retrieved from "https://commons.wikimedia.org/w/index.php?title=Category:Amino_acid_motifs&oldid=333987164" ...
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 ...
Abstract] HIERARCHICAL MOTIF VECTORS FOR AMINO ACID SEQUENCE ALIGNMENT
We present a new framework for global and localalignment of amino acid sequences based on hierarchicalmotif vectors that ... for global and local alignment of amino acid sequences based on hierarchical motif vectors that characterize local amino acid ... We then formulate different schemes for aligning amino acid sequences based on their respective motif vectors globally as well ... sequence alignment; amino acid sequence analysis;physico-chemical profiles; motif vectors; waveletdecomposition. ...
A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinson's disease | PNAS
A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinsons disease. Jill A. ... A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinsons disease ... A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinsons disease ... A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinsons disease ...
Amino Acid Motifs | Profiles RNS
"Amino Acid Motifs" by people in this website by year, and whether "Amino Acid Motifs" was a major or minor topic of these ... "Amino Acid Motifs" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical Subject ... Amino Acid Motifs*Amino Acid Motifs. *Amino Acid Motif. *Motif, Amino Acid ... Below are the most recent publications written about "Amino Acid Motifs" by people in Profiles. ...
Specific Amino Acid Substitutions in the Proline-Rich Motif of the Rhizobium meliloti ExoP Protein Result in Enhanced...
Two of seven amino acid substitutions in the proline-rich motif of ExoP affected EPS I production, indicating that most of the ... Substitution of specific amino acid residues in the proline-rich motif of the ExoP protein.To analyze the relevance of the ... Specific Amino Acid Substitutions in the Proline-Rich Motif of the Rhizobium meliloti ExoP Protein Result in Enhanced ... Specific Amino Acid Substitutions in the Proline-Rich Motif of the Rhizobium meliloti ExoP Protein Result in Enhanced ...
Occurrence of a Repeating 11-Mer Amino Acid Sequence Motif in Diverse Organisms | Bentham Science
Amino acid preferences at each position in the motif are presented, as are dot matrix sequence comparisons between several of ... Amino acid preferences at each position in the motif are presented, as are dot matrix sequence comparisons between several of ... Occurrence of a Repeating 11-Mer Amino Acid Sequence Motif in Diverse Organisms. Author(s): Leon Dure III. Department of ... Abstract: A repeating 11-mer amino acid sequence motif, first recognized in plant seed proteins, has been observed in such ...
A single amino-acid change in a highly conserved motif of gp41 elicits HIV-1 neutralization and protects against CD4 depletion
... ... We previously identified 3S, a critical conserved motif of gp41 that induces the NKp44L ligand of an activating NK receptor. In ... Generation of antibodies in mice against the W614 specific position in the 3S motif elicited a capacity to neutralize cross- ... Results: Here, we show that specific substitutions in the 3S motif reduce viral infection without affecting gp41 production, ...
Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence...
Thomsen, M. C. F., & Nielsen, M. (2012). Seq2Logo: a method for construction and visualization of amino acid binding motifs and ... Thomsen, MCF & Nielsen, M 2012, Seq2Logo: a method for construction and visualization of amino acid binding motifs and ... Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence ... Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence ...
An actin-binding site containing a conserved motif of charged amino acid residues is essential for the morphogenic effect of...
E. FRIEDERICH et al., "An actin-binding site containing a conserved motif of charged amino acid residues is essential for the ... An actin-binding site containing a conserved motif of charged amino acid residues is essential for the morphogenic effect of ... "An Actin-binding Site Containing a Conserved Motif of Charged Amino Acid Residues Is Essential for the Morphogenic Effect of ... "An Actin-binding Site Containing a Conserved Motif of Charged Amino Acid Residues Is Essential for the Morphogenic Effect of ...
A conserved 12-amino acid motif in Sall1 recruits the nucleosome remodeling and deacetylase corepressor complex
Single amino acid substitutions defined the critical amino acid peptide motif as RRKQXK-PXXF. This motif probably exhibits a ... We have identified a highly conserved 12-amino acid motif in the transcription factor Sall1 that is sufficient for the ... Single amino acid substitutions defined the critical amino acid peptide motif as RRKQXK-PXXF. This motif probably exhibits a ... We have identified a highly conserved 12-amino acid motif in the transcription factor Sall1 that is sufficient for the ...
A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinson's disease.
We found that susceptibility to PD can be explained by a specific combination of amino acids at positions 70-74 on the HLA-DRB1 ... The association of specific combinations of amino acids that participate in critical peptide-binding pockets of the HLA class ... We found that susceptibility to PD can be explained by a specific combination of amino acids at positions 70-74 on the HLA-DRB1 ... The association of specific combinations of amino acids that participate in critical peptide-binding pockets of the HLA class ...
Vibrational spectroscopy of a non-aromatic amino acid-based model peptide: Identification of the gamma-turn motif of the...
Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power. |...
Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power.. ... Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power.. ... Amino Acid Sequence, Computer Graphics, Computer Simulation, Information Systems, Models, Molecular, Protein Conformation, ... Amino acid sequence patterns suggested to characterize specific recurrent turn conformation in protein are tested as to their ...
Hierarchical motif vectors for prediction of functional sites in amino acid sequences using quasi-supervised learning
... motif vectors to represent local amino acid sequence configurations for predicting the functional attributes of amino acid ... Hierarchical motif vectors for prediction of functional sites in amino acid sequences using quasi-supervised learning. ... The motif vectors are constructed via wavelet decomposition on the variations of physico-chemical amino acid properties along ... We then formulate a prediction scheme for the functional attributes of amino acid sites in terms of the respective motif ...
The eukaryotic linear motif resource ELM: 10 years and counting
... classifying and curating information about short linear motifs (SLiMs). For ,10 years, this resource has provided the ... The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, ... Amino Acid Motifs* * Databases, Protein* * Internet * Multiprotein Complexes / chemistry * Protein Interaction Domains and ... The eukaryotic linear motif resource ELM: 10 years and counting Nucleic Acids Res. 2014 Jan;42(Database issue):D259-66. doi: ...
Amino Acid Motifs | Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence
The AIM Center is funded by NIH grant P20GM121176, and it endows the state of New Mexico and the surrounding region with a state-of-the-art biomedical center and an intellectual and technological hub for cutting-edge research. On a larger scale, the AIM Center promises to be a nationally important center for the advancement of research on autophagy. ...
Search for Functionally Significant Motifs and Amino Acid Residues of Actin | Bioinformatics Solutions Inc.
A common conserved amino acid motif module shared by bacterial and intercellular adhesins: bacterial adherence mimicking cell...
A common conserved amino acid motif module shared by bacterial and intercellular adhesins: bacterial adherence mimicking cell- ... A common conserved amino acid motif module shared by bacterial and intercellular adhesins: bacterial adherence mimicking cell- ... Short motif sequences determine the targets of the prokaryotic CRISPR defence system F. J. M. Mojica, C. Díez-Villaseñor, J. ...
Discovery of amino acid motifs for thrombin cleavage and validation using a model substrate<...
... enzyme prefers individual amino acids at each subsite in isolation or prefers to cleave combinations of amino acids as a motif ... enzyme prefers individual amino acids at each subsite in isolation or prefers to cleave combinations of amino acids as a motif ... enzyme prefers individual amino acids at each subsite in isolation or prefers to cleave combinations of amino acids as a motif ... enzyme prefers individual amino acids at each subsite in isolation or prefers to cleave combinations of amino acids as a motif ...
TriPepSVM - de novo prediction of RNA-binding proteins based on short amino acid motifs - Viral Bioinformatics Research Centre
TriPepSVM - de novo prediction of RNA-binding proteins based on short amino acid motifs. by admin · November 9, 2018. ... TriPepSVM - de novo prediction of RNA-binding proteins based on short amino acid motifs. Source: Viral Bioinformatics ... or disordered low-complexity regions of RBPs have been identified to play an important role in interactions with nucleic acids ... the 18th annual Nucleic Acids Research web server issue 2020 , #Bioinformatics Vol 48, Issue W1 , https://bit.ly/2VmTV4a ...
YUHSpace: Identification of the amino acid sequence motif of alpha-synuclein responsible for macrophage activation
Identification of the amino acid sequence motif of alpha-synuclein responsible for macrophage activation, doi: 10.1016/j.bbrc. ... YUHSpace: Identification of the amino acid sequence motif of alpha-synuclein responsible for macrophage activation. menu ... Amino Acid Motifs/genetics ; Animals ; Cell Line ; DNA Mutational Analysis ; Humans ; Macrophage Activation*/genetics ; ... Identification of the amino acid sequence motif of alpha-synuclein responsible for macrophage activation ...
Candice S. Klug, PhD | Professor | Medical College of Wisconsin
Identification of a peptide motif that potently inhibits two functionally distinct subunits of Shiga toxin | Communications...
Thus, the peptide motif demonstrated potent inhibition of two functionally distinct subunits of Stx. Watanabe-Takahashi, Tamada ... A monomeric peptide with the same motif, however, did not bind to the B-subunit pentamer. Instead, the monomer inhibited ... On the other hand, a monomeric peptide containing the same motif occupies the Stx catalytic cavity, suggesting that this ... peptide motif can inhibit two subunits of Stx. ... which has a synthetic amino acid βAla in its motif, better ...
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. ...
Plasmodesmata (eBook, 2005) [WorldCat.org]
3.3.3 Phloem Thioredoxin h 8211; charged amino acids as PD motifs --. 3.3.4 Proteolytic processing facilitates transport of ... charged amino acids as PD motifs -- 3.3.4 Proteolytic processing facilitates transport of CmPP36 -- 3.3.5 A short PD-targeting ... 3.3.5 A short PD-targeting motif in phloem HSC70 --. 3.3.6 The elusive nature of PD-targeting signals --. 3.4 Conclusions and ... motif in phloem HSC70 -- 3.3.6 The elusive nature of PD-targeting signals -- 3.4 Conclusions and future prospects -- ...
Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing...
Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing ... Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing ... Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing ... title = "Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid ...
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid...
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid ... MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs, and amino acid ... sequence motifs, and amino acid composition ...
Influenza Virus-Specific Human Antibody Repertoire Studies | The Journal of Immunology
HCDR3 amino acid motifs that are associated with influenza responses.. In some respects, the Ab fold that forms the framework ... Indeed, several specific amino acid patterns have been identified in Ab CDRs as comprising canonical motifs for interaction ... Interestingly, each of these genetic features (common V or D gene usage and convergent amino acid motifs and indels) has been ... The Ab protein remarkably mimics the interaction of the carbohydrate sialic acid by placing its amino acid structure into the ...
SequencesProteinsResiduesPeptidesHighly conservedSubstitutionsPhysico-chemicalPeptide motifResidueMeSHHierarchical motif vectorsPhylogeneticMultigene FamilyCombinations of amino acidsApproximately 70PutativeFunctionalNucleotideInteractionDegenerateAntibodiesProline-richGenesTryptophanPhosphorylationConsensusNucleic acidMutantsBiologyMutationEnzymeSerineEpitopeSubunitTargetsRepressorMinorStructuresCleavageHydrophobicSimilarityEukaryoticStructuralCriticalRecurrentGene familyEncodeHigh-molecular-weightInteractionsOrganismsEscherichiaCytoplasmic
Sequences33
- To explore the relationships between sequence and disease states or parasite phenotype, we acquired a set of DBL1α sequences from children with severe and mild malaria and developed specific algorithms to identify sequence-motifs (MOTIFF) and examined them for correlations with observed phenotypes. (pnas.org)
- We present a new framework for global and local alignment of amino acid sequences based on hierarchical motif vectors that characterize local amino acid configurations. (actapress.com)
- The motif vectors are constructed by carrying out wavelet decomposition on numeric property sequences obtained by replacing each amino acid in a sequence with their respective properties, and concatenating such profiles obtained for a large number of physico-chemical properties into a single column vector. (actapress.com)
- We then formulate different schemes for aligning amino acid sequences based on their respective motif vectors globally as well as locally subject to measures of statistical significance. (actapress.com)
- Experiment results indicate that the motif vectors accurately capture the amino acid composition at and around individual sites along sequences and allow associating sequence segments sharing similar functional attributes. (actapress.com)
- Although the amino acid sequences of the N-terminal ExoP domain and the similar proteins were only weakly conserved, these proteins displayed structural similarities, since they were characterized by two putative transmembrane helices and a conserved proline-rich amino acid motif located on the periplasmic side, very close to the second membrane helix ( 2 , 6 , 28 , 32 ). (asm.org)
- Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. (dtu.dk)
- The motif vectors are constructed via wavelet decomposition on the variations of physico-chemical amino acid properties along the sequences. (iyte.edu.tr)
- E-values refer to the significance of each motif found within the CIR sequences. (nih.gov)
- The frequency (percentage) of CIR sequences within the whole repertoire, clade A1 or whole sub-families A and B containing each motif is shown. (nih.gov)
- A) Similarity plot of the aligned capsid amino acid sequences of 64 enterovirus prototype strains. (asm.org)
- Primer sequences are shown directly below the amino acid motif sequences. (asm.org)
- Three conserved protein motifs were identified by aligning the VP3 and VP1 sequences of prototype EV strains. (asm.org)
- In this system, nucleotide sequences which are at least 75% identical (85% amino acid identity) are considered to represent strains of the same serotype ( 12 - 14 , 19 , 20 ). (asm.org)
- Deduced amino acid sequences constantly showed the toxic motifs. (mdpi.com)
- A comparison of the amino acid sequences and phylogenetic analysis of 31 full-length cDNAs of maize ( Zea mays ) AQPs shows that they comprise four different groups of highly divergent proteins. (plantphysiol.org)
- Amino acid sequence identities vary from 16% to 100%, but all sequences share structural motifs and conserved amino acids necessary to stabilize the two loops that form the aqueous pore. (plantphysiol.org)
- We report here a whole genome analysis of the olfactory receptor genes of Bos taurus using conserved OR gene-specific motifs and known OR protein sequences from diverse species. (biomedcentral.com)
- Identifying motifs in biological sequences is an important challenge in biology. (merlot.org)
- To our knowledge all currently available methods search motifs in protein sequences at the amino acid level, sometimes. (merlot.org)
- To our knowledge all currently available methods search motifs in protein sequences at the amino acid level, sometimes allowing degenerate motifs to comply with point variations [1, 2]. (merlot.org)
- Given a set of protein sequences known to be involved in a common biological system (positive set) and a set of protein sequences known not to be involved in that system (negative set) our method is able to identifiy motifs that are frequent in positive sequences while infrequent or absent in negative sequences. (merlot.org)
- These motifs did have some predictive ability in searching for the known epitopes among a set of decoy sequences. (mcponline.org)
- PEST motifs are sequences rich in Pro, Glu, Asp, Ser and Thr which have been proposed to constitute protein instability determinants. (cnrs.fr)
- AC: A Compression Tool for Amino Acid Sequences. (bioportfolio.com)
- art method for lossless compression of amino acid sequences. (bioportfolio.com)
- The Variability of Amino Acid Sequences in Hepatitis B Virus. (bioportfolio.com)
- OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs. (bioportfolio.com)
- A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. (bioportfolio.com)
- Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences. (bioportfolio.com)
- The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. (bioportfolio.com)
- Alignment of sequences around putative catalytic residues in known cutinases and this enzyme indicated that the three residues (S119, D199, H214) which form a catalytic triad in lipases, esterases, and serine proteases are conserved in this enzyme along with the consensus sequence lipase box GXSXG motif around a catalytic serine (Fig. 1 ). (asm.org)
- Phylogenetic analysis using full-length amino acid sequences of functionally characterized BAHD enzymes by D'Auria (2006) and Stewart et al. (wikipedia.org)
Proteins17
- A repeating 11-mer amino acid sequence motif, first recognized in plant seed proteins, has been observed in such diverse organisms as the nematode Caenorhabditis elegans and the eubacteria Haemophilus influenzae and Dienococcus radiodurans. (eurekaselect.com)
- Amino acid preferences at each position in the motif are presented, as are dot matrix sequence comparisons between several of the proteins harboring the repeating motif. (eurekaselect.com)
- Although implicated in plant abiotic stress tolerance, no molecular function for the proteins carrying the motif has yet been uncovered. (eurekaselect.com)
- This motif probably exhibits a more general role in regulating gene expression, since other proteins containing this domain, including all Sall family members and an unrelated zinc finger protein Ebfaz, mediate transcriptional repression and associate with NuRD. (escholarship.org)
- Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power. (ac.be)
- Amino acid sequence patterns suggested to characterize specific recurrent turn conformation in protein are tested as to their predictive power in a database containing 75 proteins of known structure. (ac.be)
- About 10% of the fungal genes induced during the biotrophic colonization encoded putative small secreted proteins (SSP), including several lectin-like proteins and members of a P. indica -specific gene family (DELD) with a conserved novel seven-amino acids motif at the C-terminus. (pubmedcentralcanada.ca)
- VQ motif-containing (VQ) proteins are plant-specific proteins that interact with WRKY transcription factors and play important roles in plant growth, development and stress response. (biomedcentral.com)
- The CsVQ proteins all contained the typical conserved motif FxxhVQxhTG, and most proteins were localized in the nucleus. (biomedcentral.com)
- Most divergent are the small and basic integral proteins in which the first of the two highly conserved Asn-Pro-Ala motifs of the pore is not conserved, but is represented by alanine-proline-threonine or alanine-proline-serine. (plantphysiol.org)
- Finding motifs specific to proteins involved in the same process can help deciphering the determinants of their fate and thus be used in identifying new candidate proteins involved in important biological systems. (merlot.org)
- The identified motifs can then be used to mine the wealth of protein data now available, in order to identify new previously uncharacterized proteins involved in biological processes of importance. (merlot.org)
- The APOBEC3 proteins are a mammalian-specific family of nucleic acid cytidine deaminases that block retroviral infection. (mdpi.com)
- A BLAST search revealed that the deduced amino acid sequence of this protein did not exhibit homology with any of the known lipases, and the enzyme was found to be weakly (12 to 20%) homologous to proteins belonging to the cutinase family. (asm.org)
- In this study, we have identified 11 Arabidopsis genes encoding novel proteins, termed RICs (for Rop-interactive CRIB motif-containing proteins), that contain a CRIB (for Cdc42/Rac-interactive binding) motif required for their specific interaction with GTP-bound Rop1. (elsevier.com)
- Here, using a customized workflow, we report genes encoding GAST proteins, identify novel motifs and evolutionary patterns contributing to the subfunctionalization of GAST domains, and explore functional conservation across diverse plant groups. (plantphysiol.org)
- Thus, our study identifies GAST s and their encoded proteins, uncovers their structure, novel motifs, and evolutionary pattern among plants, and suggests their functional conservation. (plantphysiol.org)
Residues8
- An actin-binding site containing a conserved motif of charged amino acid residues is essential for the morphogenic effect of villin. (ugent.be)
- In this paper, the functional significance of this conserved motif is further studied by the analysis of mutants in conserved residues Asn387, Ser388, and Gly391. (neb.com)
- Here, we further attenuated WNV by mutating the asparagine to serine or glutamine in addition to mutating other residues in the NS1 130-132 glycosylation motif. (utmb.edu)
- Reference: Identification of amino acid residues in the human immunodeficiency virus type-1 reverse transcriptase tryptophan-repeat motif that are required for subunit interaction using infectious virions. (neb.com)
- Here, we analyzed the contributions of amino acid residues comprising the Trp-motif to RT subunit interaction and function. (neb.com)
- Our results reveal important inter- and intra-subunit interactions of residues in the Trp-motif. (neb.com)
- We propose a method that allows to identify emerging motifs based both on conservation of amino acids and on the physico-chemical properties of these residues. (merlot.org)
- Interestingly, acute depletion of phosphatidylinositol 4-phosphate (PtdIns4P) at the Golgi complex reduced GAP-43 membrane binding, highlighting a new, pivotal role for this anionic lipid and supporting the idea that basic amino acid residues are involved in the electrostatic interactions between GAP-43 and membranes of the Golgi complex where they are S-acylated. (portlandpress.com)
Peptides4
- Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. (dtu.dk)
- One of these peptides, MMA-tet (containing the following motif, Met-Met-Ala-Arg-Arg-Arg-Arg), inhibits the major Stx family members (e.g. (nature.com)
- By contrast, HC-10 did not react with six additional peptides, each bearing motif amino acid substitutions present in HC-10-not-reactive HLA-I allospecificities. (jimmunol.org)
- Though the epitopes were not directly evident, subtle motifs were found among the top binding peptides for each antibody. (mcponline.org)
Highly conserved1
- We have identified a highly conserved 12-amino acid motif in the transcription factor Sall1 that is sufficient for the recruitment of NuRD. (escholarship.org)
Substitutions5
- The production of the acidic exopolysaccharide succinoglycan (EPS I) by Rhizobium meliloti exoP * mutants expressing an ExoP protein lacking its C-terminal cytoplasmic domain and by mutants characterized by specific amino acid substitutions in the proline-rich motif (RX 4 PX 2 PX 4 SPKX 9 IXGXMXGXG) located from positions 443 to 476 of the ExoP protein was analyzed. (asm.org)
- Specific substitutions within the 3S peptide motif were prepared by directed mutagenesis. (nih.gov)
- Here, we show that specific substitutions in the 3S motif reduce viral infection without affecting gp41 production, while decreasing both its capacity to induce NKp44L expression on CD4(+) T cells and its sensitivity to autologous NK cells. (nih.gov)
- Single amino acid substitutions defined the critical amino acid peptide motif as RRKQXK-PXXF. (escholarship.org)
- To test whether UIM-mediated binding results in substrate preference, these scientists generated a panel of USP25 mutants carrying substitutions of functional amino acids in UIMs and analyzed their interaction with and catalytic activity toward Lys48- or Lys63-linked ubiquitin chains. (eurekalert.org)
Physico-chemical1
- At a given position in the sequence, the nature and physico-chemical properties of amino acids in protein families is more conserved than the amino acid itself. (merlot.org)
Peptide motif1
- Thus, the peptide motif demonstrated potent inhibition of two functionally distinct subunits of Stx. (nature.com)
Residue3
- Mutants in phi 29 DNA polymerase residue Tyr390 of this conserved motif had been previously described to be affected in DNA-dependent dNTP binding. (neb.com)
- 1. A peptide consisting of the amino acid sequence of FIG. 1 (SEQ ID NO:68) from about the lysine residue at amino acid 676 to about the valine residue at amino acid 1255. (google.com)
- The Histidine in this motif has also been shown to act as a catalytic residue in many BAHD enzymes. (wikipedia.org)
MeSH1
- Amino Acid Motifs" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (umassmed.edu)
Hierarchical motif vectors1
- We propose hierarchical motif vectors to represent local amino acid sequence configurations for predicting the functional attributes of amino acid sites on a global scale in a quasi-supervised learning framework. (iyte.edu.tr)
Phylogenetic2
- The amino acid motifs and phylogenetic analyses indicated that MeGSTs were divided into 9 classes. (springer.com)
- Phylogenetic analysis revealed that the GAST-Cysteine Rich1 motif evolved early in the S. moellendorffii GAST, which further acquired subfunctionalization through successive conjugation of other motifs and remained conserved across plants, as supported by their collinearity. (plantphysiol.org)
Multigene Family1
- Interestingly, the PTL motif is conserved in other members of the fos multigene family. (cnrs.fr)
Combinations of amino acids2
- The association of specific combinations of amino acids that participate in critical peptide-binding pockets of the HLA class II molecule implicates antigen presentation in PD pathogenesis and provides further support for genetic control of neuroinflammation in disease. (escholarship.org)
- While the subsite specificity of thrombin is understood, it is not clear whether the enzyme prefers individual amino acids at each subsite in isolation or prefers to cleave combinations of amino acids as a motif. (monash.edu)
Approximately 701
- The regulatory domain of MyoD is approximately 70 amino acids in length and includes both a basic DNA binding motif and a bHLH dimerization motif. (fishersci.com)
Putative4
- The C-terminal cytoplasmic domain contains a putative ATP binding motif ( 6 ). (asm.org)
- We also found that PopP2 harbors a putative eukaryotic transcriptional repressor motif (ethylene-responsive element binding factor-associated amphiphilic repression or EAR), which is known to be involved in the recruitment of transcriptional co-repressors. (frontiersin.org)
- We have previously shown that FYCO1 binds to LC3B via a 19-amino acid sequence containing a putative core LC3-interacting region (LIR) motif. (rcsb.org)
- The putative 622-amino acid protein has a leucine-zipper motif at its N-terminus. (wikipedia.org)
Functional6
- We then formulate a prediction scheme for the functional attributes of amino acid sites in terms of the respective motif vectors using the quasi-supervised learning algorithm that carries out predictions for all sites in consideration using only the experimentally verified sites. (iyte.edu.tr)
- The tetravalent peptide has a synthetic amino acid, β−Ala, in each functional motif. (nature.com)
- Two major sub-families were identified, which have been named A and B. Members of each sub-family displayed different amino acid motifs, and were thus predicted to have undergone functional divergence. (nih.gov)
- To address the functional significance of the LIR motif of FYCO1, we generated FYCO1 knock-out cells that subsequently were reconstituted with GFP-FYCO1 WT and LIR mutant constructs. (rcsb.org)
- Our data show that FYCO1 requires a functional LIR motif to facilitate efficient maturation of autophagosomes under basal conditions, whereas starvation-induced autophagy was unaffected. (rcsb.org)
- Gibberellic Acid Stimulated Transcript-Related 9 ) suggests hormonal regulation, novel roles in seed germination, and functional conservation among diverse plant groups. (plantphysiol.org)
Nucleotide1
- We show that a DEEDh (the five catalytic amino acids) motif drives nucleotide excision. (rcsb.org)
Interaction4
- Specific PfEMP1-DBL1α amino acid motifs correlated with rosetting and severe malaria, with motif location corresponding to distinct regions of receptor interaction. (pnas.org)
- The propensity of both the side chain and the backbone carbonyls of the polyproline type II helix to participate in the interface interaction makes it an excellent recognition motif. (hindawi.com)
- FBPs mediate protein-protein interaction with roughly 50 amino acids within their structural motifs. (news-medical.net)
- We found that mutation of critical basic amino acids drastically reduced membrane interaction and hence S-acylation of GAP-43. (portlandpress.com)
Degenerate3
- Finally, phosphorylation motifs (standard, degenerate, and multiply phosphorylated) were extracted from the data set with the Motif-X algorithm. (nih.gov)
- Consensus degenerate primers were designed from a conserved VP3 motif and a distal VP1 motif for the first PCR. (asm.org)
- Consensus-degenerate hybrid oligonucleotide primers were designed from an internal VP1 motif and used with the same distal VP1 motif for the second, seminested PCR step. (asm.org)
Antibodies2
- Generation of antibodies in mice against the W614 specific position in the 3S motif elicited a capacity to neutralize cross-clade viruses, notable in its magnitude, breadth, and durability. (nih.gov)
- 15. The diagnostic composition of claim 14, wherein said compounds are nucleic acid molecules or antibodies. (freepatentsonline.com)
Proline-rich1
- Intermolecular interactions mediated by proline-rich motifs (PRMs) are observed in many facets of the immune response. (hindawi.com)
Genes4
- Genome-wide distribution of the repressed genes of Lactobacillus helveticus CM4 in response to amino acids on the genome map ( a ) and locations from the origin with the repressive effects ( b ). a Location of the repressed genes by amino acids on a previously reported physical map of Lactobacillus helveticus CM4 chromosomal DNA [ 20 ]. (biomedcentral.com)
- b Locations of the repressed genes from the origin and the repressive effects by amino acids in CM4. (biomedcentral.com)
- Gibberellic Acid Stimulated Transcript ( GAST )-like genes encode small polypeptides, some of which have been implicated in diverse biological processes regulating plant growth and development. (plantphysiol.org)
- Computational modeling predicts that these GAST genes are regulated by several factors, including the phytohormones gibberellin and abscisic acid, through conserved cis-motifs present in their promoters, and that they might act as signaling molecules in a complex feedback loop. (plantphysiol.org)
Tryptophan1
- The second conserved motif is DFGWG (Aspartic acid, Phenylalanine, Glycine, Tryptophan, Glycine) and it is typically found near the carboxyl terminus of the protein and is thought to participate in CoA binding (D'Auria, 2006). (wikipedia.org)
Phosphorylation2
- Together, these findings suggest that agrin-induced phosphorylation of the β subunit motif increases the stoichiometry of rapsyn binding to the AChR, thereby helping to stably cluster the receptor and anchor it at high density in the postsynaptic membrane. (jneurosci.org)
- Because of the large size of the data set, both novel and known phosphorylation motifs were extracted using the Motif-X algorithm, including those representative of potential ordered phosphorylation events. (nih.gov)
Consensus1
- Consensus amino acid motifs are shown. (asm.org)
Nucleic acid1
- A ribosome only binds to the RER once a specific protein-nucleic acid complex forms in the cytosol. (wikipedia.org)
Mutants2
- [email protected]#To establish 293T cell lines stably expressing Calpain-cleavage related α3 cytoplasmic tail mutants, and to explore the effect of amino acid motifs in integrin β3 cytoplasmic tail on αⅡbβ3-mediated cell function. (bvsalud.org)
- Cnx1E Asp274 mutants accumulate the Moco precursor adenylated molybdopterin, thus providing the molecular framework required for subsequent research work devoted to elucidate the mechanism behind molybdate insertion into the MPT dithiolene motif which is intrinsically tied to Moco formation. (portlandpress.com)
Biology1
- 10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear motifs. (nih.gov)
Mutation2
- Remarkably, mutation of the EAR motif disabled PopP2 avirulence function as measured by the development of hypersensitive response, electrolyte leakage, defense marker gene expression and bacterial growth in Arabidopsis. (frontiersin.org)
- Interestingly, a mutation at a SUMO- interacting motif (SIM), but not the catalytic sites within the mature Trx2 protein, completely blocks Trx2 processing with no effect on Trx2 mitochondrial targeting. (frontiersin.org)
Enzyme3
- Irp5 shows 41% similarity to EntE, the 2,3-dihydroxybenzoic acid-activating enzyme utilized in enterobactin synthesis of Escherichia coli . (asm.org)
- This enzyme could effectively degrade the high-molecular-weight compound polylactic acid, as well as other biodegradable plastics, including polybutylene succinate, poly (ε-caprolactone), and poly(3-hydroxybutyrate). (asm.org)
- Members of this enzyme family typically share two conserved amino acid motifs. (wikipedia.org)
Serine1
- Overall, we showed that changing the asparagine of the NS1 130 glycosylation motif to a serine or glutamine attenuated WNV further than the asparagine to alanine substitution. (utmb.edu)
Epitope3
- Spot technique-based experiments showed that 667 recognizes a linear epitope of 12 amino acids located in the variable region A of the receptor binding domain. (cnrs.fr)
- Alanine scanning experiments showed that six amino acids within the epitope are critical for MAb binding. (cnrs.fr)
- In rheumatoid arthritis (RA), the shared epitope (SE), a five-amino acid sequence motif encoded by RA-associated HLA - DRB1 alleles, is the single most significant genetic risk factor. (wn.com)
Subunit1
- A monomeric peptide with the same motif, however, did not bind to the B-subunit pentamer. (nature.com)
Targets1
- The incipient formation of cisplatin-derived complexes with the recognized biological amino acid targets L-histidine (His) and L-methionine (Met) has been investigated revealing the primary platination event to be mainly directed at the Nπ atom of the imidazole side chain of His and to the thiomethyl sulfur of Met. (unich.it)
Repressor1
- Importantly, our data also indicate that the PopP2 conserved repressor motif could contribute to the effector accumulation in plant cells. (frontiersin.org)
Minor1
- This graph shows the total number of publications written about "Amino Acid Motifs" by people in this website by year, and whether "Amino Acid Motifs" was a major or minor topic of these publications. (umassmed.edu)
Structures3
- motifs d'acides aminés (fr) Three-dimensional protein structural elements that are composed of a combination of secondary structures. (wikimedia.org)
- Many of these patterns are found to be associated with local structures that differ from the motifs originally used to derive them. (ac.be)
- Tiemann, B., Gerardy-Schahn, R., and Bakker, H. (2013) LARGE2 generates the same xylose and glucuronic acid containing glycan structures as LARGE. (mh-hannover.de)
Cleavage4
- To investigate whether preferred peptide motifs for cleavage could be identified for thrombin, we exposed a phage-displayed peptide library to thrombin. (monash.edu)
- The results revealed that thrombin selected for amino acid motifs in cleavage sites. (monash.edu)
- The contribution of these hypothetical motifs to substrate cleavage efficiency was further investigated using the B1 IgG-binding domain of streptococcal protein G as a model substrate. (monash.edu)
- Introduction of further P(3)-P(1) and P(1)-P(1) -P(3) amino acid motifs into the loop region yielded greater cleavage efficiencies, suggesting that the susceptibility of a protein substrate to cleavage by thrombin is influenced by these motifs, perhaps because of cooperative effects between subsites closest to the scissile peptide bond. (monash.edu)
Hydrophobic1
- The signals for GAP-43 S-acylation are confined to the first 13 amino acids, including the S-acylatable cysteines 3 and 4 embedded in a hydrophobic region, followed by a cluster of basic amino acids. (portlandpress.com)
Similarity1
- phi 29 DNA polymerase shares with other alpha-like DNA polymerases several regions of amino acid similarity. (neb.com)
Eukaryotic1
- The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). (nih.gov)
Structural2
- Structural analysis of crystals of mammalian AQPs and amino acid sequence comparisons of all AQPs show that they have six membrane-spanning alpha helices with N and C termini that face the cytosol. (plantphysiol.org)
- The structural modification includes addition or deletion of a leucine-based motif or parts thereof. (google.com)
Critical3
- We previously identified 3S, a critical conserved motif of gp41 that induces the NKp44L ligand of an activating NK receptor. (nih.gov)
- Our study reveals that a unique SUMO-interacting motif of Trx2 is critical for its mitochondrial processing and subsequent anti-oxidant/antisenescence activities. (frontiersin.org)
- Glycerol molecules move in a single file through an equally narrow amphipathic channel in which the NPA motifs also play a critical role. (plantphysiol.org)
Recurrent1
- and (b) a selective expansion of Vδ1 cells bearing recurrent junctional amino acid motifs. (jci.org)
Gene family1
- Members of Gibberellic Acid Stimulated Transcript ( GAST ) gene family are regulated by GA and encode small polypeptides that have a C-terminal domain of ∼60 amino acids. (plantphysiol.org)
Encode1
- [10] The first 5-30 amino acids polymerized encode a signal peptide , a molecular message that is recognized and bound by a signal recognition particle (SRP). (wikipedia.org)
High-molecular-weight1
- The irp1 gene consists of 9,486 bp capable of encoding a 3,161-amino-acid high-molecular-weight protein 1 (HMWP1) polypeptide with a predicted mass of 384.6 kDa. (asm.org)
Interactions2
- Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange formats. (nih.gov)
- Furthermore, unstructured or disordered low-complexity regions of RBPs have been identified to play an important role in interactions with nucleic acids. (4virology.net)
Organisms1
- Leon Dure III, " Occurrence of a Repeating 11-Mer Amino Acid Sequence Motif in Diverse Organisms", Protein & Peptide Letters (2001) 8: 115. (eurekaselect.com)
Escherichia1
- Betha, AK, Williams, AM & Martinis, SA 2007, ' Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing activity ', Biochemistry , vol. 46, no. 21, pp. 6258-6267. (illinois.edu)
Cytoplasmic2
- ExoP consists of 786 amino acids and can be divided into an N-terminal domain (positions 1 to 481), mainly located in the periplasm, and a C-terminal cytoplasmic domain (positions 482 to 786) ( 6 ). (asm.org)
- [email protected]#293T cell lines stably co-expressing human wild type integrin αⅡb and full length β3 or mutant β3, including β3-ΔNITY (β3 cytoplasmic tail NITY motif deleted), β3-Δ754 (β3 cytoplasmic tail TNITYRGT motif deleted) and β3-Δ759 (β3 cytoplasmic tail RGT motif deleted) were established. (bvsalud.org)