AnatomyOrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation ScienceHealth Care
DNA-Binding ProteinsMolecular Sequence DataBase SequenceDNAProtein BindingBinding SitesAmino Acid SequenceTranscription FactorsDNA, Single-StrandedDimerizationPromoter Regions, GeneticTranscription, GeneticEscherichia coliCarrier ProteinsNuclear ProteinsPoly(A)-Binding ProteinsBacterial ProteinsProtein Structure, TertiaryRepressor ProteinsMutationDNA HelicasesPyrimidine DimersCell LineModels, MolecularSequence Homology, Amino AcidDNA ReplicationRecombinant Fusion ProteinsCloning, MolecularRecombinant ProteinsReplication Protein AViral ProteinsOligodeoxyribonucleotidesHeLa CellsTranscriptional ActivationPlasmidsTrans-ActivatorsElectrophoretic Mobility Shift AssayZinc FingersProtein ConformationCell NucleusKineticsGene Expression RegulationDNA, ViralEscherichia coli ProteinsSequence AlignmentElectrophoresis, Polyacrylamide GelRNA, MessengerNucleic Acid ConformationPoly TMacromolecular SubstancesTacrolimus Binding ProteinsMolecular WeightTransfectionDNA PrimersRNA-Binding ProteinsSaccharomyces cerevisiae ProteinsMutagenesis, Site-DirectedLeucine ZippersCCAAT-Enhancer-Binding ProteinsPoly(A)-Binding Protein IUltraviolet RaysDNA FootprintingDNA, BacterialBinding, CompetitiveHelix-Turn-Helix MotifsSaccharomyces cerevisiaeProtein MultimerizationNFI Transcription FactorsConsensus SequenceFungal ProteinsRegulatory Sequences, Nucleic AcidCrystallography, X-RayProtein Structure, SecondaryInsulin-Like Growth Factor Binding ProteinsY-Box-Binding Protein 1Chromatography, AffinityStructure-Activity RelationshipSubstrate SpecificitySequence DeletionMutagenesisCells, CulturedOligonucleotidesDNA, ComplementaryGene Expression Regulation, BacterialHomeodomain ProteinsCross-Linking ReagentsDNA, FungalConserved SequenceSignal TransductionDNA RepairPhosphorylationDNA PrimaseCyclic AMP Response Element-Binding ProteinPolydeoxyribonucleotidesHeterogeneous-Nuclear RibonucleoproteinsHelix-Loop-Helix MotifsBasic-Leucine Zipper Transcription FactorsFatty Acid-Binding ProteinsGene ExpressionGenes, Reporter
SequencesGenesMotifHelix-loop-ResiduesHetero-dimersHeterodimersTranscription factorRecognitionReplicationGeneNuclearBacterialSpecificityTetramerAffinityRELBInteractMutationCrystalMutationsRepressorConformationalTranscriptional activatorsInteractionsBZIPCell proliferationLigandsCoiled coilLocalizationComplexesRegulatoryRoadblocksHistoneP105MotifsConsensusMismatchTumorDouble-strandedScaffoldAbnormalChromosomalPhosphorylationVivoStructuralSitesStableDomainMoleculeP100MolecularTyrosineCatalysisRecombinantActivate transcriptionAbstract
Sequences11
  • It is notably thanks to these sequences that TDP-43 importantly binds to its own mRNA regulates its very own solubility and polymerization. (wikipedia.org)
  • We have recently turned our attention to a new class of controller proteins (exemplified by C.Csp231I) that have quite novel features, including a much larger DNA-binding site with an 18 bp (~60 Å) spacer between the two palindromic DNA-binding sequences and a very different recognition sequence from the canonical GACT/AGTC. (port.ac.uk)
  • The transcription factor AmrZ utilizes multiple DNA binding modes to recognize activator and repressor sequences of Pseudomonas aeruginosa virulence genes. (wakehealth.edu)
  • Upon binding to 17beta-estradiol or related ligands, the encoded protein forms homo- or hetero-dimers that interact with specific DNA sequences to activate transcription. (cancerindex.org)
  • We analyzed respective gene promoters' sequences using in silico methods for identification of transcription binding sites, mainly in the NF-κB- and IRF-coding genes. (biomedcentral.com)
  • Transcriptional pausing is highly regulated by the template DNA and nascent transcript sequences. (bvsalud.org)
  • The 72-amino acid TEA DNA binding domains in mTEAD-2, 3, and 4 are approximately 99% homologous to the same domain in mTEAD-1, and all four proteins bind specifically to the same DNA sequences in vitro with a Kd value of 16-38 nM DNA. (embl-heidelberg.de)
  • Our results have uncovered differences between acute and chronic TNF signals that may arise through variation in signal input, specific requirements for Rel family dimers, divergence in kB consensus sequences and differences in affinities of protein-DNA binding. (biomedcentral.com)
  • Dimers of leucine zipper proteins recognize short, inverted, repeat sequences. (neighborshateus.com)
  • ROESY, NOE spectroscopy in the operator DNA sequences aimed at removing the rotating frame. (lu.se)
  • DNA sequences used for studies of uncomplexed and complexed trp operator. (lu.se)
Genes13
  • Important regulatory factors, TFs bind to the promoter regions of target genes and activate or inhibit their transcription. (biomedcentral.com)
  • The dimer attaches to specific areas of DNA and helps control the activity of particular genes. (medlineplus.gov)
  • AmrZ beta-sheet residues are essential for DNA binding and transcriptional control of Pseudomonas aeruginosa virulence genes. (wakehealth.edu)
  • Our in silico findings report that there is cross-regulation between both pathways at the level of gene transcription regulation, mediated by the presence of binding sites for both factors in promoters of genes essential for these pathways. (biomedcentral.com)
  • At the molecular level, pitavastatin induced expression of the cyclin dependent kinase (CDK) inhibitor p21 in a cholesterol independent manner, blocked repressive phosphorylation of the Retinoblastoma tumor suppressor protein at CDK targeted sites, and reduced expression of E2F target genes required for progression through the G1/S boundary. (oncotarget.com)
  • The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. (abcam.com)
  • MYC/MAX heterodimers bind to specific DNA elements, designated as E-boxes, located in the promoter regions of target genes mediating either activation or repression of transcription. (ashpublications.org)
  • These genes were uncovered on the basis of similarity to the DNA binding domain [ ( PUBMED:9504043 ) ] of Mus musculus (Mouse) Brachyury (T) gene product, which similarity is the defining feature of the family. (embl-heidelberg.de)
  • Mice contain at least four, and perhaps five, genes with the same TEA DNA binding domain (mTEAD genes). (embl-heidelberg.de)
  • Here, we report that the guanine nucleotide-binding protein (G protein)-coupled receptor-activated WD-repeat Gβ interacts with the glucocorticoid receptor (GR), comigrates with it into the nucleus and suppresses GR-induced transactivation of the glucocorticoid-responsive genes. (rupress.org)
  • By interrogation of extended fragments of genomic sequence from 66 TNF-induced genes, we have mapped the DNA binding consensus sequence sites for different transcription factors. (biomedcentral.com)
  • For the classical NF-κB DNA binding motif GGGRNNYYCC our analysis revealed multiple kB 'hits' in 55/66 TNF-induced genes. (biomedcentral.com)
  • We therefore suggest a new mechanism involving a cofactor that is regulated as well as recruited by one of the master genes to bind to the antagonistic partner that is necessary for bistability and hence switch-like behavior. (lu.se)
Motif6
  • MITF gene mutations that cause Tietz syndrome either delete or change a single protein building block (amino acid) in an area of the MITF protein known as the basic motif region. (medlineplus.gov)
  • When the gene is overexpressed, the plant is less sensitive to environmental signals and flowers earlier.The LEAFY protein has two conserved domains: the DNA binding domain, a Helix-Turn-Helix motif buried inside a unique 7-helix fold and a Sterile Alpha Motif. (definitions.net)
  • A basic region helix-loop-helix leucine zipper motif (bHLH-Zip) protein, designated Max, specifically associates with c-Myc, N-Myc and L-Myc proteins. (ihcworld.com)
  • How is the leucine zipper motif related to DNA binding? (neighborshateus.com)
  • The Leucine Zipper Motif Mediates Both DNA Binding and Protein Dimerization. (neighborshateus.com)
  • In occurs through the inhibition of DNA binding of cognate cis- hematopoiesis there exist several lineage branch points with regulatory motif while in the other case DNA binding is unaffected identified key transcription factors and external signals [3-5]. (lu.se)
Helix-loop-3
  • 1 MYC is a basic helix-loop-helix-leucine zipper transcription factor that dimerizes with the related protein MAX. (ashpublications.org)
  • Extra-macrochaetae sequesters these basic-region-helix-loop-helix transcription factors as heterodimers inefficient for binding to DNA. (biologists.com)
  • If Extramacrochaetae par-ticipates in cell specification by dimerizing with basic-region-helix-loop-helix proteins, the variety of defects and tissues affected by the insufficiency of extramacrochaetae suggests that helix-loop-helix proteins are involved in many embryonic developmental processes. (biologists.com)
Residues11
  • an unstructured C-terminal domain encompassing residues 274-414 (CTD), which contains a glycine-rich region, is involved in protein-protein interactions, and harbors most of the mutations associated with familial amyotrophic lateral sclerosis. (wikipedia.org)
  • The protein sequence also has a nuclear localization signal (NLS, residues 82-98), a former nuclear export signal (NES residues 239-250) and 3 putative caspase-3 cleavage sites (residues 13, 89, 219). (wikipedia.org)
  • The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
  • Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
  • Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
  • Essential amino acid residues in the single-stranded DNA-binding protein of bacteriophage T7. (wakehealth.edu)
  • The Arg-62 residues of the TREX1 exonuclease act across the dimer interface contributing to catalysis in the opposing protomers. (wakehealth.edu)
  • The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. (embl.de)
  • Leucine zipper domains are made up of two motifs: a basic region that recognizes a specific DNA sequence and a series of leucines spaced 7 residues apart along an α-helix (leucine zipper) that mediate dimerization. (neighborshateus.com)
  • The Leucine Zipper and the Basic DNA-Binding Domain (bZIP) This leucine zipper facilitates the dimerization of the protein by interdigitation of two leucine containing helices on different molecules and these residues form the buried subunit interface of the coiled-coil dimer. (neighborshateus.com)
  • These basic residues interact in the major groove of the DNA, forming sequence-specific interactions. (neighborshateus.com)
Hetero-dimers2
  • This family of proteins comprises two subfamilies that share a DNA-binding and dimerization domain called the Rel homology domain (RHD) [ 4 ] and form homo- or hetero- dimers. (oncotarget.com)
  • Murre and Baltimore, 1992 , reviews) characteristic of a large family of transcriptional reg-ulators that function as homo-or hetero-dimers. (biologists.com)
Heterodimers3
  • Max can also form heterodimers with at least two additional bHLH-Zip proteins, Mad and Mxi1 and Mad-Max dimers have been shown to repress transcription through interaction with mSin3. (ihcworld.com)
  • p100 and p105 can however undergo limited proteolysis to generate p52 and p50, respectively, which can form heterodimers with Rel proteins to form transcriptional activators [ 5 ]. (oncotarget.com)
  • Gel shift assays demonstrate consistent differences in the binding of Rel family proteins to DNA, since acute TNF stimulation induces formation of a dominant DNA binding complex comprising p65:p50 heterodimers (complex I), while the binding capacity of a second complex (complex II), which may include p50:p50 homodimers, is increased in nuclear extracts of chronic TNF-stimulated cells. (biomedcentral.com)
Transcription factor4
  • On the basis of this action, the MITF protein is called a transcription factor. (medlineplus.gov)
  • The variety of AP-1 dimer configurations confer versatility to this transcription factor in regulating numerous physiological (cell proliferation, differentiation, apoptosis, migration) and pathological activities (cancer, inflammation, transplant rejection) in the cell. (indigobiosciences.com)
  • So far, the team has fused the halves of SpDamID to 30 different transcription factor proteins, and documented the outcomes. (cincinnatichildrens.org)
  • Basic-region leucine zipper (bZIP) proteins are one of the largest transcription factor families that regulate a wide range of cellular functions. (neighborshateus.com)
Recognition9
  • The winged helix domains are at opposite ends of the extended coiled coil with two putative DNA-recognition helices separated by 55A and rotated by 83 degrees. (rcsb.org)
  • An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
  • Using X-ray crystallography, the structure of the protein in complex with its 21 bp DNA-recognition sequence was solved to 1.8 Å resolution, and the molecular basis of sequence recognition in this class of proteins was elucidated. (port.ac.uk)
  • An unusual aspect of the promoter sequence is the extended spacer between the dimer binding sites, suggesting a novel interaction between the two C-protein dimers when bound to both recognition sites correctly spaced on the DNA. (port.ac.uk)
  • The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response. (wakehealth.edu)
  • DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG). (wakehealth.edu)
  • This protein forms a stable, tetrameric oligomer with two binding sites and can produce a loop of DNA between recognition sites separated along the length of a DNA molecule. (bvsalud.org)
  • Further analysis suggests that the observed reduction in UV survival is consistent with the hypothesis that enhanced nontarget DNA affinity results in reduced pyrimidine dimer-specific recognition and/or binding. (elsevierpure.com)
  • This analysis illustrates two regions on the PfNapS dimer as the possible sites for histone recognition. (biomedcentral.com)
Replication8
  • The production of material needs to be compatible with volume, area, and shape constraints of the growing vesicle, the rates of growth and DNA replication need to be tuned to the timing of cell division, and spatial cues need to be in place to ensure the proper distribution of genetic material. (basyc.nl)
  • Both missense and nonsense mutations result in an incorrect, and likely dysfunctional, polypeptide structure, and can be caused by a number of various errors in DNA replication. (ukessays.com)
  • Tautomeric shifts are one of the most prominent errors observed in DNA replication and result in base-pair mismatching. (ukessays.com)
  • Sometimes mutations occur during replication due to interactions of DNA with the environment. (ukessays.com)
  • This protein helps fix errors that are made when DNA is copied (DNA replication) in preparation for cell division. (medlineplus.gov)
  • This complex identifies locations on the DNA where errors have been made during DNA replication. (medlineplus.gov)
  • A shortage of this protein eliminates mismatch repair activity and prevents the proper repair of DNA replication errors. (medlineplus.gov)
  • Chromatin is highly dynamic, a characteristic that is vital in regulating nuclear processes such as transcription and replication which require access to DNA. (biomedcentral.com)
Gene14
  • TAR DNA-binding protein 43 (TDP-43, transactive response DNA binding protein 43 kDa) is a protein that in humans is encoded by the TARDBP gene. (wikipedia.org)
  • This gene provides instructions for making a protein that plays a role in the development, survival, and function of certain types of cells. (medlineplus.gov)
  • In a wide variety of bacterial restriction-modification systems, a regulatory `controller' protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. (port.ac.uk)
  • In recent years, developmental biologists have gathered rough snapshots of protein activity by using a combination of chromatin immunoprecipitation and next-generation gene sequencing (ChIP-seq). (cincinnatichildrens.org)
  • Additionally, PIAS proteins can also recruit corepressors and histone deacetylases to inhibit STAT-mediated gene expression. (creativebiomart.net)
  • Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 are associated with systemic lupus erythematosus. (wakehealth.edu)
  • The gene product contains an N-terminal DNA binding domain and C-terminal ligand binding domain and is localized to the nucleus, cytoplasm, and mitochondria. (cancerindex.org)
  • What does this gene/protein do? (cancerindex.org)
  • The MSH2 gene provides instructions for making a protein that plays an essential role in repairing DNA. (medlineplus.gov)
  • The MSH2 protein joins with one of two other proteins, MSH6 or MSH3 (each produced from a different gene), to form a two-protein complex called a dimer. (medlineplus.gov)
  • MSH2 gene variants result in near or complete loss of MSH2 protein production. (medlineplus.gov)
  • MSH2 gene variants involved in Lynch syndrome may cause the production of an abnormally short or inactive MSH2 protein or prevent the production of any protein from one copy of the gene. (medlineplus.gov)
  • Because there is some functional MSH2 protein produced from the normal copy of the gene, mismatch repair activity in Lynch syndrome is reduced but not absent, as it is in CMMRD syndrome (described above). (medlineplus.gov)
  • We show that in vivo E2 binds to its site even under conditions where it does not activate a reporter gene. (pasteur.fr)
Nuclear4
  • Stimulation of TLRs (Toll-Like Receptors) by a pathogen induces activation of signal transduction cascades, which leads to translocation of nuclear factor-κB (NF-κB) to the nucleus [ 1 ], activation of interferon regulatory factors 3/7 (IRF3/7) and/or activator protein-1 (AP-1), which cooperate to induce transcription of various cytokines such as alpha/beta interferon (IFN-α/β) to counteract infection [ 2 - 4 ]. (biomedcentral.com)
  • Myc proteins are nuclear proteins with relatively short half lives. (ihcworld.com)
  • IκBζ, an atypical member of the nuclear IκB family of proteins, is expressed at low levels in most resting cells, but is induced upon stimulation of Toll-like/IL-1 receptors through an IRAK1/IRAK4/NFκB-dependent pathway. (oncotarget.com)
  • Preliminary data indicate that chronic but not acute TNF stimulation also induces RelB nuclear translocation and DNA binding. (biomedcentral.com)
Bacterial4
  • Kinemage 2 shows the extensive coiling of a bacterial protein called tropomyosin (from PDB file, 2TMA). (wustl.edu)
  • The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix (HTH) domains binding to successive major grooves of the DNA. (uni-konstanz.de)
  • ParABS partition systems, comprising the centromere-like DNA sequence parS, the parS -binding ParB-CTPase and the nucleoid-binding ParA-ATPase, ensure faithful segregation of bacterial chromosomes and low-copy-number plasmids. (biorxiv.org)
  • Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. (cdc.gov)
Specificity2
Tetramer3
  • The X-ray structure of the casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. (elifesciences.org)
  • Probable transcriptional regulator protein that binds to DNA as dimer and tetramer, but not as a monomer. (lu.se)
  • The repeating unit of chromatin is the nucleosome, formed from two histone H2A-H2B dimers and one histone H3-H4 tetramer around which 147 bp of DNA are wrapped [ 1 ]. (biomedcentral.com)
Affinity5
  • Ubiquitin-like domain are usually associated with a greater affinity for RNA/DNA. (wikipedia.org)
  • This hitherto unseen mode of DNA binding by TrmBL2 seems to arise from nonoptimal protein-DNA contacts made by its four HTH domains resulting in a low-affinity, nonspecific binding to DNA. (uni-konstanz.de)
  • Thus, despite binding with high affinity, these repressors are not effective roadblocks to transcription. (bvsalud.org)
  • Previous studies indicate that a decrease in the affinity of endonuclease V for nontarget DNA results in a decreased ability to scan DNA and a concomitant decrease in the ability to enhance UV survival in repair-deficient Escherichia coli. (elsevierpure.com)
  • This study was designed to question the contrasting effect of an increase in the affinity of endonuclease V for nontarget DNA. (elsevierpure.com)
RELB2
  • NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52. (abcam.com)
  • The first subfamily of proteins (c-Rel, RelB, p65/RelA) contains a C-terminal transactivation domain. (oncotarget.com)
Interact4
  • This allows experts to mark each chromosome location where the two proteins interact. (cincinnatichildrens.org)
  • PIAS proteins interact with activated STAT dimers and inhibit STAT-mediated transcription. (creativebiomart.net)
  • Oxidising agents also interact with DNA from the environment by altering the base-pairing ability of nucleotides with chemical modifications. (ukessays.com)
  • PfNapL and PfNapS do not interact with each other and unlike PfNapL, PfNapS is able to deposit histones onto DNA [ 6 ]. (biomedcentral.com)
Mutation1
  • The TREX1 exonuclease R114H mutation in Aicardi-Goutières syndrome and lupus reveals dimeric structure requirements for DNA degradation activity. (wakehealth.edu)
Crystal8
  • A U-bend model is proposed for this tetrameric complex, based on the results of gel-mobility assays, hydrodynamic analysis and the observation of key contacts at the interface between dimers in the crystal. (port.ac.uk)
  • Defects in DNA degradation revealed in crystal structures of TREX1 exonuclease mutations linked to autoimmune disease. (wakehealth.edu)
  • Crystal structure of RNA-DNA duplex provides insight into conformational changes induced by RNase H binding. (wakehealth.edu)
  • The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. (uni-konstanz.de)
  • The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. (embl.de)
  • Extensive sequence and structural comparisons were done with the crystal structures available for NAP/SET family of proteins. (biomedcentral.com)
  • C, trpO decamer of the crystal structure of uncomplexed trp oper- ator DNA (Shakked et al. (lu.se)
  • Nucleotides for which water-mediated pro- tein-DNA contacts with the bases were observed in the co-crystal structures are encircled with a continuous line. (lu.se)
Mutations4
  • Grill C, Bergsteinsdottir K, Ogmundsdottir MH, Pogenberg V, Schepsky A, Wilmanns M, Pingault V, Steingrimsson E. MITF mutations associated with pigment deficiency syndromes and melanoma have different effects on protein function. (medlineplus.gov)
  • The TREX1 double-stranded DNA degradation activity is defective in dominant mutations associated with autoimmune disease. (wakehealth.edu)
  • Scope includes mutations and abnormal protein expression. (cancerindex.org)
  • In order to tackle mutations caused by mis-incorporated, inserted or deleted bases, cells exhibit the use of a system known as DNA mismatch repair. (ukessays.com)
Repressor4
  • This is a simple yet powerful experimental approach to investigate such interactions between DNA and proteins as demonstrated by experiments with the lac repressor. (bvsalud.org)
  • For example, the phage 186 CI repressor forms a wheel of seven dimers wrapped in DNA with specific binding sites, while phage λ CI repressor dimers bind to two well-separated sets of operators, forming a DNA loop. (bvsalud.org)
  • Wrapped and looped topologies induced by these scaffolded, cooperatively bound repressor oligomers did not form significantly better roadblocks to transcription. (bvsalud.org)
  • Some proteins, like the lac repressor (LacI), mediate long-range loops that alter DNA topology and create torsional barriers. (bvsalud.org)
Conformational3
  • This process of polymerization into dimers, larger forms or just stabilizing monomers is dependent on TDP-43 conformational equilibrium between monomers, homodimers and oligomers. (wikipedia.org)
  • DNA binding induces active site conformational change in the human TREX2 3'-exonuclease. (wakehealth.edu)
  • Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. (embl.de)
Transcriptional activators1
  • Different dimer combinations act as transcriptional activators or repressors, respectively. (abcam.com)
Interactions4
  • Indeed, dimers are formed by head-to-head interactions between NTDs, and the polymer thus obtained allows for pre-mRNA splicing. (wikipedia.org)
  • Possible DNA-binding interactions are discussed on the basis of comparisons to other winged helix proteins. (rcsb.org)
  • Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
  • Kornberg 7 has presented that the interactions between DNA and histones are involved in chromosome packaging in the cell nucleus. (nature.com)
BZIP5
Cell proliferation3
  • c-Myc-, N-Myc- and L-Myc-encoded proteins function in cell proliferation, differentiation and neoplastic disease. (ihcworld.com)
  • virtually every tissue expresses at least one family member, consistent with a critical role for TEAD proteins in either cell proliferation or differentiation. (embl-heidelberg.de)
  • Recently, a large number of signaling proteins reported play an important key role in the process of LPLI-induced cell proliferation, probably due to the fact that the molecular events they are involved in are the basic response of the cells to extracellular stimuli. (biomedcentral.com)
Ligands2
  • The excursions of the bead may reflect the intrinsic flexibility and/or topology of the polymer as well as changes due to the action activity of ligands that bind the polymer. (bvsalud.org)
  • Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. (lu.se)
Coiled coil3
  • The 95 amino acid residue protein contains a winged helix DNA-binding domain with an extended C-terminal alpha-helix that leads to dimerization by forming a two-stranded, antiparallel coiled-coil rod. (rcsb.org)
  • The coiled coil contains a rare aspartate residue (D69) in the normally hydrophobic d position of the heptad repeat, with two aspartate-lysine (d-g') interhelical ion pairs in the symmetrical dimer. (rcsb.org)
  • 5.2 {ce lys 27} 10.793 14.34 -6.426 {nz lys 27} 11.577 15.578 -6.283 {ca leu 29} P .8 13.434 -3.964 {cb leu 29} .692 14.17 -2.63 {cg leu 29} -.5 15.08 -2.588 {cd1 leu 29} -1.573 14.266 -1.91 {cg leu 29} P -.5 15.081 -2.588 {cd2 leu 29} -.185 16.36 -1.8 @kinemage 2 @caption Calpha trace of the coiled coil protein, tropomyosin. (wustl.edu)
Localization1
  • GFP-fused PfNapS fusion protein targeting indicates cellular localization of PfNapS in the parasite nucleus. (biomedcentral.com)
Complexes5
  • Crystallization of protein-DNA complexes. (wakehealth.edu)
  • F-plasmid partition complexes containing ParB F and parS F move by generating and following a local concentration gradient of nucleoid-bound ParA F . However, the process through which ParB F activates ParA F -ATPase has not been defined. (biorxiv.org)
  • Atomic force microscopy was used to measure transcription elongation by Escherichia coli RNA polymerase (RNAP) through these protein complexes. (bvsalud.org)
  • Small angle neutron scattering (SANS) provides unique insight into biomacromolecular complexes by combining solvent contrast variation (H2O:D2O exchange) with either natural contrast between different classes of biomolecules (proteins, RNA/DNA, lipids/detergents) and/or by applying artificial contrast, i.e. deuteration of specific biomolecules. (lu.se)
  • In a first couple of examples, I will show how distance and shape restraints from SANS have helped to improve the uniqueness of structural models for two multi-protein-RNA complexes, in combination with NMR restraints and building blocks from crystallography [1, 2]. (lu.se)
Regulatory1
  • These regulatory proteins also modulate the DNA-binding properties of STATs by facilitating SUMOylation of the dimers. (creativebiomart.net)
Roadblocks1
  • RNA polymerases (RNAPs) must transit through protein roadblocks to produce full-length RNAs. (bvsalud.org)
Histone3
  • Nucleosome assembly proteins (NAPs) are histone chaperones that are crucial for the shuttling and incorporation of histones into nucleosomes. (biomedcentral.com)
  • Fluorescence spectroscopy was performed to identify histone-binding sites on PfNapS. (biomedcentral.com)
  • Histone chaperones are proteins that regulate the interaction of histones with other proteins and DNA and also prevent the highly basic histones from forming inappropriate aggregates [ 2 , 3 ]. (biomedcentral.com)
P1051
  • The second subfamily of proteins (p105 and p100) has a C-terminal region that contains multiple copies of ankyrin repeats, instead of a transactivation domain, and can bind to and inhibit Rel proteins. (oncotarget.com)
Motifs3
  • Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. (embl.de)
  • They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. (embl.de)
  • The presence of three sequence motifs in the c-Myc COOH terminus, including the leucine zipper, the helixloop-helix and a basic region, provided initial evidence for a sequence-specific binding function. (ihcworld.com)
Consensus2
  • Most ParABS systems have multiple copies of a ParB dimer binding consensus sequence that collectively constitute a parS site. (biorxiv.org)
  • The T-box is defined as the minimal region within the T-box protein that is both necessary and sufficient for sequence-specific DNA binding, all members of the family so far examined bind to the DNA consensus sequence TCACACCT. (embl-heidelberg.de)
Mismatch2
  • Small molecule induction of MSH2-dependent cell death suggests a vital role of mismatch repair proteins in cell death. (wakehealth.edu)
  • It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. (nih.gov)
Tumor2
  • Negative regulators, such as SOCS proteins, act as tumor suppressors by inhibiting aberrant Jak/STAT signaling. (creativebiomart.net)
  • Hepatocyte growth factor receptor (c-Met), a member of tyrosine protein kinase receptors (TPKR), is phosphorylated during LPLI-induced proliferation, but tumor necrosis factor alpha (TNF-alpha) receptor has not been affected. (biomedcentral.com)
Double-stranded3
  • We therefore hypothesized that the selective induction of DNA double-stranded breaks in the X chromosome during male meiosis might be a potential strategy to distort the sex ratio of the progeny towards male mosquitoes, if the normal production of Y-bearing gametes was unaffected ( Fig. 1a ). (nature.com)
  • Exonuclease TREX1 degrades double-stranded DNA to prevent spontaneous lupus-like inflammatory disease. (wakehealth.edu)
  • While the deoxyribose phosphate groups of the double-stranded DNA (dsDNA) used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. (uni-konstanz.de)
Scaffold2
  • This 'zipper' acts as a scaffold for some proteins which bind DNA in higher organisms. (wustl.edu)
  • DNA can act as a scaffold for the cooperative binding of protein oligomers. (bvsalud.org)
Abnormal1
Chromosomal1
  • As these proteins bind to chromosomal sites, they deliver instructions that direct a cell's fate and function. (cincinnatichildrens.org)
Phosphorylation2
  • Fluorescent antibodies specific for cell surface markers can be combined with markers of apoptosis, proliferation and protein phosphorylation to determine which cell subsets respond to various stimuli or treatments. (bdbiosciences.com)
  • Phosphorylation of some proteins, such as Stat5, results in dimer formation that masks the phosphorylated epitope of interest. (bdbiosciences.com)
Vivo4
  • Nucleotide excision repair in human cells: fate of the excised oligonucleotide carrying DNA damage in vivo. (ncsu.edu)
  • It binds DNA as a dimer and its binding site has been identified both in vivo and in vitro. (definitions.net)
  • We propose that such reciprocating motion also enables RNAP to break protein-DNA contacts holding RNAP back during promoter escape and RNA chain elongation, facilitating productive transcription in vivo. (bvsalud.org)
  • In an attempt to understand the molecular basis of this synergy we carried out genomic footprinting to monitor the binding in vivo of native or mutant E2 proteins to different templates in yeast. (pasteur.fr)
Structural2
  • SCOP: Structural Classification of Proteins and ASTRAL. (berkeley.edu)
  • SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
Sites9
  • Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
  • Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
  • There is an urgent need for computational tools that can rapidly and reliably identify DNA-binding sites in DNA-binding proteins. (nature.com)
  • As intuitively expected, assisting forces facilitated, and opposing forces hindered, RNAP passage through LacI bound to natural operator sites. (bvsalud.org)
  • The most effective enhancer in cleavage stage mouse embryos depends on DNA binding sites for TEF-1, the prototype for a family of transcription factors that share the same TEA DNA binding domain. (embl-heidelberg.de)
  • The papillomavirus E2 protein only activates transcription strongly when two or more of its binding-sites, each of which bind an E2 dimer, are present upstream of a minimal promoter. (pasteur.fr)
  • Binding occurs at each site independently of the number of sites and even in the absence of the activation domain. (pasteur.fr)
  • Facilitated one-dimensional diffusion is a general mechanism utilized by several DNA-interactive proteins as they search for their target sites within large domains of nontarget DNA. (elsevierpure.com)
  • T4 endonuclease V is a protein which scans DNA in a nonspecifically bound state and processively incises DNA at ultraviolet (UV)-induced pyrimidine dimer sites. (elsevierpure.com)
Stable1
  • Formation of stable dimers in solution is demonstrated by both analytical ultracentrifugation and differential scanning calorimetry. (rcsb.org)
Domain4
  • Taxonomic distribution of proteins containing ZnF_C4 domain. (embl.de)
  • The complete taxonomic breakdown of all proteins with ZnF_C4 domain is also avaliable . (embl.de)
  • Click on the protein counts, or double click on taxonomic names to display all proteins containing ZnF_C4 domain in the selected taxonomic class. (embl.de)
  • Taxonomic distribution of proteins containing TBOX domain. (embl-heidelberg.de)
Molecule1
  • All bases in DNA exist as tautomers - different chemical forms of the molecule in which protons are in different positions - but tend to exist in their more common 'keto' form. (ukessays.com)
P1001
  • This protein is the full-length p52 subunit and partial p100 subunit. (abcam.com)
Molecular3
  • Wang and his coworkers 12 investigated the discriminative power of three sequence features from protein sequence, including the side chain pKa value, the hydrophobicity index and the molecular mass of an amino acid. (nature.com)
  • We combine structure-based protein engineering and molecular genetics to restrict the activity of the potentially toxic endonuclease to spermatogenesis. (nature.com)
  • Protein structures are invaluable for biochemical studies and for mechanical or molecular mechanics calculations have become the understanding of how proteins work. (lu.se)
Tyrosine1
  • Key negative regulators of this pathway include Suppressors of Cytokine Signaling (SOCS), Protein Inhibitors of Activated STATs (PIASs), and protein tyrosine phosphatases (PTPs). (creativebiomart.net)
Catalysis1
  • 5'-exonuclease structure suggests a mechanism for efficient nonprocessive DNA catalysis. (wakehealth.edu)
Recombinant1
  • Creative BioMart offers a wide range of products and services related to Jak/STAT pathway research, including recombinant proteins, antibodies, and assay kits, to facilitate the study of these negative regulators and their potential applications in various fields. (creativebiomart.net)
Activate transcription1
  • In contrast, analysis of the chromatin structure around the E2 binding-site(s) showed that a pronounced change in chromatin structure occurs under conditions in which E2 dimers activate transcription synergistically. (pasteur.fr)
Abstract1
  • Abstract - With a growing global population, there is an urgent need to improve the health and productivity of animals that provide high quality protein in the form of meat, milk, and eggs. (elevateventures.com)