• We report here that SRE1, a gene encoding a GATA-type protein, bound to promoter sequences of genes involved in siderophore biosynthesis. (nih.gov)
  • Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (hindawi.com)
  • Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (hindawi.com)
  • This generally yields a large library of DNA sequences, including some that were bound by the transcription factor directly, some that were bound indirectly via interactions with other molecules, and some false positives (such as cases of nonspecific binding). (ucsc.edu)
  • Identification of Nucleic Acid High Affinity Binding Sequences of Proteins by SELEX Philippe Bouvet 12. (nhbs.com)
  • Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. (embl-heidelberg.de)
  • They anchor themselves and their partner proteins to DNA at binding sites in genetic regulatory sequences, bringing together the components that are needed to make gene expression happen. (mit.edu)
  • the majority of human transcription factors contain an ARM-like region between their DNA and protein binding regions, and these sequences were conserved across animal species. (mit.edu)
  • Elucidation of the hetero-dimeric binding activity of LasR and RhlR proteins with the promoter DNA and the role of a specific Phe residue during the biosynthesis of HCN synthase from opportunistic pathogen Pseudomonas aeruginosa. (bvsalud.org)
  • Till date, there is no report that deals with the binding interactions of the RhlR-LasR heterodimer with the promoter DNA region of the hcnABC operon . (bvsalud.org)
  • We, for the first time , tried to analyse the binding modes of the RhlR-LasR heterodimer with the promoter DNA regions. (bvsalud.org)
  • From our work , we could predict the importance of a specific amino acid residue Phe214 from RhlR which might be considered to have the desired specificity to bind to the promoter DNA . (bvsalud.org)
  • The mechanism whereby NM23 regulates gene expression is proposed to entail DNA-binding and subsequent alterations in promoter DNA structure. (embl.de)
  • The chicken infectious anemia virus (CAV) gene promoter fused to the gene for enhanced green fluorescent protein (EGFP) was used to measure virus activity in response to estrogen. (usda.gov)
  • The virus promoter-enhancer DNA sequence was also found to bind some of the proteins that recongnize a consensus estrogen response element (ERE) (Miller et al. (usda.gov)
  • Deletions at the 3' end of the long promoter that left the E box intact did not restore promoter activity. (usda.gov)
  • These findings indicate that the CAV promoter activity can be repressed directly or indirectly by COUP-TF1 and dEF1. (usda.gov)
  • Expression of enhanced green fluorescent protein (EGFP) under control of the promoter-enhancer of chicken infectious anemia virus (CAV) is increased in an estrogen receptor-enhanced cell line when treated with estrogen. (usda.gov)
  • This promoter-enhancer also binds unidentified proteins that recognize a consensus estrogen response element (ERE) (Miller et al. (usda.gov)
  • In this sense, we aim to characterize the behaviour of different promoters of genes involved in biofilm regulation under different conditions and to search for possible new DNAbinding proteins associated with their promoter regions. (usp.br)
  • May act in a coactivator-like fashion through protein-protein interactions by contacting factors binding to the proximal MHC class II promoter, to elements of the transcription machinery, or both. (lu.se)
  • Alternatively it may activate HLA class II transcription by modifying proteins that bind to the MHC class II promoter. (lu.se)
  • In differentiating neuroblastoma cells, HASH-1 is down-regulated, and there is coincident up-regulation of the transcriptional repressor HES-1, which is known to bind the HASH-1 promoter. (lu.se)
  • In front of every gene is a DNA sequence called a promoter. (lu.se)
  • Transcription factors bind alongside the promoter and set off the gene expression. (lu.se)
  • The activity of the promoter can therefore be regulated differently in different cells. (lu.se)
  • Here we investigated the DNA binding specificity of Brh2 in more detail using oligonucleotide substrates. (cornell.edu)
  • 2012 ), generalizing the observation that hotspot localization is determined by the DNA-binding specificity of the zinc finger array (Grey et al. (springer.com)
  • Phage-assisted continuous evolution has been adapted to the development of TALENs with better DNA-binding activity and specificity. (genengnews.com)
  • But now it has been used to continuously evolve DNA-binding domains called TALENs (transcription activator-like effector nucleases) with altered or improved DNA-binding specificity. (genengnews.com)
  • The new work appeared August 10 in Nature Methods, in an article entitled, "Continuous directed evolution of DNA-binding proteins to improve TALEN specificity. (genengnews.com)
  • Here we present DNA-binding phage-assisted continuous evolution (DB-PACE) as a general approach for the laboratory evolution of DNA-binding activity and specificity," wrote the authors. (genengnews.com)
  • DB-PACE brings the power of continuous evolution to bear on improving the activity and specificity of a variety of DNA-binding proteins. (genengnews.com)
  • Furthermore, DB-PACE coupled with in vitro specificity profiling represents a new systematic approach to removing specific off-target activities of TALENs, and it may be used to facilitate generation of highly specific genome engineering tools for therapeutic applications. (genengnews.com)
  • We are investigating how Pbx and Meis proteins contribute to the specificity of Hox function in development and how disruption of their activities leads to neoplasia. (stanford.edu)
  • As the SEC can regulate the transcriptional activity of RNA polymerase II, it was hypothesized that these MLL-fusions induce aberrant regulation of transcriptional elongation on MLL-target genes 14 . (nature.com)
  • In the developing male (XY) gonad, sex-determining region of the Y (SRY) protein acts to up-regulate expression of the related gene, SOX9 , a transcriptional regulator that in turn initiates a downstream pathway of testis development, whilst also suppressing ovary development. (plos.org)
  • Researchers can now provide a picture of how proteins regulate genetic expression at the atomic level. (sciencedaily.com)
  • 1) Characterize novel families of oncoproteins (Pbx and Meis) that dimerize with and regulate the DNA binding properties of Hox proteins. (stanford.edu)
  • Transcription factors help to regulate gene expression-turning genes on or off and dialing up or down their level of activity-often in partnership with the proteins that they bind. (mit.edu)
  • Perilipin 5 (PLIN5) is a lipid-droplet-associated protein that coordinates intracellular lipolysis in highly oxidative tissues and is thought to regulate lipid metabolism in response to phosphorylation by protein kinase A (PKA). (uci.edu)
  • Changes in DNA methylation were especially prominent in genes that regulate the activity of neurons and the connectivity between them. (medscape.com)
  • Witt said it was also "fascinating that among those genes that showed the strongest changes in DNA methylation levels in our study, two genes were previously reported to regulate behavioral aspects of cocaine intake in rodent experiments. (medscape.com)
  • Even if the DNA sequence - the set of genes - is the same in all cells, only certain genes are expressed, i.e. only information from certain genes is copied (transcribed) and used to build protein structures or regulate processes. (lu.se)
  • This gene encodes a member of the chromodomain/helicase/DNA-binding domain family of chromatin remodeling enzymes. (nih.gov)
  • CHD chromatin remodelling enzymes and the DNA damage response. (nih.gov)
  • It has therefore been proposed that the oncogenic activity of MLL-fusion proteins depends on chromatin targeting functions exerted by the MLL N-terminus in combination with other functional properties encoded by the fusion partners 6 . (nature.com)
  • One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
  • DSB sites are preferentially located within chromatin loops, while several proteins that are required for DSB formation (Rec114, Mei4, and Mer2) localize on the chromosome axis (Blat et al. (springer.com)
  • Site-Directed Cleavage of DNA by Protein-Fe(II) EDTA Conjugates within Model Chromatin Complexes David R. Chafin and Jeffrey J. Hayes 11. (nhbs.com)
  • The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. (embl-heidelberg.de)
  • The protein structure that surrounds the DNA, chromatin, largely comprises histone proteins and can be open or closed and thus allow or prevent factors binding to the DNA. (lu.se)
  • Hydrophobicity was one of the most important physicochemical properties, due to the fact that it is involved in protein interactions, for example, by forming hydrophobic cores. (hindawi.com)
  • We present the first comprehensive survey of protein-protein interactions of seven distantly related MLL-fusion proteins. (nature.com)
  • In 'DNA-Protein Interactions: Principles and Protocols, Third Edition', this vital subject is brought up to date with protocols exploring the most cutting-edge developments in the field, including in vivo and genome-wide interaction techniques. (nhbs.com)
  • Comprehensive and authoritative, 'DNA-Protein Interactions: Principles and Protocols, Third Edition' serves as an ideal guide for all those exploring this dynamic, essential, and increasingly affordable area of research. (nhbs.com)
  • Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions Manon Gaudreault, Marie-Eve Gingras, Maryse Lessard, Steeve Leclerc, and Sylvain L. Guerin 3. (nhbs.com)
  • Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper Athanasios G. Papavassiliou 14. (nhbs.com)
  • Enhancing our understanding of how molecular interactions at the atomic level have consequences for the genetic activity of a cell brings new avenues for medical research. (sciencedaily.com)
  • The clues have been there all along, but I think earlier work was so focused on the DNA and protein interactions that they didn't consider RNA. (mit.edu)
  • FLIM-FRET analysis of protein-protein interactions showed that PLIN5 S155 phosphorylation regulates PLIN5 interaction with adipose triglyceride lipase at the lipid droplet, but not with α-β hydrolase domain-containing 5. (uci.edu)
  • Studying interactions, we noted that all four Id proteins could dimerize with E47 or E2-2, but not with HASH-1 or dHAND. (lu.se)
  • While the field is still in its relative infancy, Dr. Hubbard said human clinical trials involving sequence-specific DNA-editing agents are already underway. (genengnews.com)
  • Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting Simon Labbe, Jean-Francois Harrisson, and Carl Seguin 13. (nhbs.com)
  • Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. (wikidata.org)
  • We present evidence that zinc supplementation to HIPK2i cells increased p53 reactivity to conformation-sensitive PAb1620 (wild-type conformation) antibody and restored p53 sequence-specific DNA binding in vivo and transcription of target genes in response to Adriamycin treatment. (aacrjournals.org)
  • We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein. (hindawi.com)
  • the WD motif is responsible for a protein-protein interaction. (embl.de)
  • Each DNA binding domain recognizes and interacts with DNA that matches a specific nucleotide pattern, or motif. (ucsc.edu)
  • These motifs tend to be short and degenerate, so even when the DNA binding motif is known, one cannot generally predict where a given transcription factor may bind. (ucsc.edu)
  • instead, it binds RNA from a region called an arginine-rich motif (ARM) that is unstructured but has a high affinity for RNA. (mit.edu)
  • DEC-205 (CD205), a member of the macrophage mannose receptor protein family, is the prototypic endocytic receptor of dendritic cells, whose ligands include phosphorothioated cytosine-guanosine (CpG) oligonucleotides, a motif often seen in bacterial or viral DNA. (uci.edu)
  • Here we report a role for the phylogenetically ancient mitogen-activated protein kinase (MAPK) signalling pathway in mouse sex determination. (plos.org)
  • The byg mutation is an A to T transversion causing a premature stop codon in the gene encoding MAP3K4 (also known as MEKK4), a mitogen-activated protein kinase kinase kinase. (plos.org)
  • This mutant, which we called boygirl ( byg ), was shown to contain an early stop codon that disrupts the autosomal gene encoding MAP3K4, a component of the mitogen-activated protein kinase (MAPK) signaling pathway. (plos.org)
  • These oligomeric proteins exhibit nucleoside diphosphate kinase (NDPK) activity that catalyzes nonsubstrate specific conversions of nucleoside diphosphates to nucleoside triphosphates. (embl.de)
  • Acute leukemias induced by MLL chimeric oncoproteins are among the subset of cancers distinguished by a paradoxical dependence on GSK-3 kinase activity for sustained proliferation. (stanford.edu)
  • Homeodomain-interacting protein kinase-2 (HIPK2) is a positive regulator of p53 oncosuppressor function. (aacrjournals.org)
  • The most frequently analyzed family member, p38 alpha, also known as SAPK2a and MAPK14, was initially purified as a kinase critical to the signaling cascade linking IL-1 to MAPKAPK-2 and the small heat shock protein HSP27. (rndsystems.com)
  • Dps dodecamers can condense DNA in vitro through a cooperative binding mechanism. (wikipedia.org)
  • We are studying the effects and consequences of protein fusion on the transcriptional and transforming activities of these proteins using in vitro and animal models. (stanford.edu)
  • No DNA binding of in vitro translated CIITA was detected. (lu.se)
  • Finally, we demonstrate that Polycomb proteins and associated epigenetic marks are crucial for the control of the replication timing of the INK4a/ARF locus during senescence. (plos.org)
  • Epigenetic changes mainly take place through chemical modification of DNA (DNA methylation) and histones, the proteins around which the DNA helix winds itself. (lu.se)
  • Epigenetic modifications of the histone proteins, such as acetylation or methylation, affect how tightly the DNA is packed around the histones and thus how accessible the DNA sequence is. (lu.se)
  • As well as DNA methylation, there are also other epigenetic mechanisms such as modification of histone proteins. (lu.se)
  • For example, some proteins activate transcription by recruiting RNA polymerase, some repress transcription by suppressing this recruitment, and others insulate proximal regions from the activity of nearby transcriptional activators or repressors. (ucsc.edu)
  • Polymerase chain reaction: locates and makes copies of parts of the DNA contained in the castor bean plant. (cdc.gov)
  • TCF4 gene mutations disrupt the protein's ability to bind to DNA and control the activity of certain genes. (medlineplus.gov)
  • These gene mutations typically do not affect the TCF4 protein's ability to bind to other proteins. (medlineplus.gov)
  • The TCF4 protein's inability to bind to DNA and control the activity of certain genes, particularly those genes involved in nervous system development and function, contributes to the signs and symptoms of Pitt-Hopkins syndrome. (medlineplus.gov)
  • The inhibition of STAT3 protein's ability to bind to DNA is an attractive treatment for aggressive carcinomas. (hawaii.edu)
  • E proteins made by the viral genome promote the activation of host DNA replication mechanisms that can then be used by the virus during its own replication. (medscape.com)
  • Before genome editing can be used more widely for clinical purposes, researchers need to develop better-targeted DNA-binding proteins. (genengnews.com)
  • High numbers of repetitive DNA elements (RepMPs), designated RepMP1, RepMP2/3, RepMP4, and RepMP5, comprise ≈8% of the M. pneumoniae genome and play essential roles in survival niches of M. pneumoniae by engaging in recombination events to generate surface antigen diversity ( 5 ). (cdc.gov)
  • P1 adhesin causes antigenic variation between clinical strains as a result of homologous recombination between RepMP2/3 and RepMP4 domains located within their open reading frames and at repetitive DNA elements at other sites in the bacterial genome ( 8 ). (cdc.gov)
  • Tat increases the transcription of HIV's RNA genome by binding to the virus' RNA and then recruiting cellular machinery to it. (mit.edu)
  • The telomeres are the DNA-protein structures at the ends of eukaryotic chromosomes, which serve to protect and stabilize the genome. (lu.se)
  • during stationary phase, Dps binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and protected from diverse damages. (wikipedia.org)
  • Chromosome 9 is made up of about 141 million DNA building blocks (base pairs) and represents approximately 4.5 percent of the total DNA in cells. (medlineplus.gov)
  • Chromosome 9 likely contains 800 to 900 genes that provide instructions for making proteins. (medlineplus.gov)
  • Theoretical and empirical studies have shown that it is likely that the transcription factors bind to a chromosome wherever they encounter one and then glide along the DNA in search of their binding sites. (sciencedaily.com)
  • The TCF4 protein is part of a group of proteins known as E-proteins. (medlineplus.gov)
  • Transcription factors are a group of proteins that are needed for a gene to start being copied to RNA, i.e. for transcription to start. (lu.se)
  • Moreover, we show that the Polycomb protein BMI1 interacts with CDC6, an essential regulator of DNA replication in eukaryotic cells. (plos.org)
  • DNA repair proteins that include the bacterial MutS DNA mismatch-binding protein and its eukaryotic homologs that function in DNA MISMATCH REPAIR and recombination of DNA during MEIOSIS. (bvsalud.org)
  • DNA-binding proteins from starved cells (DPS) are bacterial proteins that belong to the ferritin superfamily and are characterized by strong similarities but also distinctive differences with respect to "canonical" ferritins. (wikipedia.org)
  • DPS proteins are part of a complex bacterial defence system that protects DNA against oxidative damage and are distributed widely in the bacterial kingdom. (wikipedia.org)
  • The latter might seem impossible, as an arbitrary transcription factor normally exists in just a handful of copies inside a bacterial cell, and one of them has to find a specific binding site on the DNA spiral, which contains some five million base pairs, in order to turn a gene on or off," says Erik Marklund, one of the lead authors of the new study. (sciencedaily.com)
  • it occurs when mannose-binding lectin (MBL), a serum protein, binds to mannose, fucose, or N -acetylglucosamine groups on bacterial cell walls, yeast walls, or viruses. (msdmanuals.com)
  • This role involves its DNA-binding domain, which is composed of a tandem array of zinc fingers, and PRDM9-dependent trimethylation of histone H3 at lysine 4. (springer.com)
  • 2010 ). PRDM9 includes several functional domains, such as a DNA-binding zinc finger array, a histone lysine methyltransferase PR/SET (PRDI-BF1 and RIZ1 homology) domain, and a Krüppel-associated box (KRAB)-related domain. (springer.com)
  • When cells enter senescence the binding to RD of both PRC1 and PRC2 complexes is lost leading to a decreased level of histone H3K27 trimethylation (H3K27me3). (plos.org)
  • This loss is accompanied with an increased expression of the histone demethylase Jmjd3 and with the recruitment of the MLL1 protein, and correlates with the expression of the Ink4a/Arf genes. (plos.org)
  • L genes encode viral capsid proteins. (medscape.com)
  • Once the inhibitor enters cells, it keeps the IRF5 protein from traveling to the cell's nucleus, which houses DNA and activating genes that may encode proteins involved in an autoimmune attack. (lupusresearch.org)
  • HPV is now known to be a small deoxyribonucleic acid (DNA) virus that infects epithelial cells and causes a variety of skin lesions. (medscape.com)
  • Interestingly, the expression of two IκB kinases (IKK)-α/β, the degradation of cytosolic IκB-β inhibitor and the NF-κB deoxyribonucleic acid binding activity were markedly reduced after FP treatment in both CF and non-CF bronchial epithelial cells. (ersjournals.com)
  • The effects of corticosteroids are predominantly mediated by the inhibition of NF-κB deoxyribonucleic acid (DNA)-binding activity, which controls genes encoding inflammatory cytokines, chemokines and adhesion molecules in respiratory epithelial cells 10 - 13 . (ersjournals.com)
  • In S. cerevisiae , this interaction is at least in part provided by Spp1 that directly interacts with both methylated H3K4 near DSB sites and the axis-localized protein Mer2 (Acquaviva et al. (springer.com)
  • This protein interacts with another protein called core binding factor beta or CBFβ (produced from the CBFB gene), which helps RUNX1 bind to DNA and prevents it from being broken down. (medlineplus.gov)
  • The Y-linked sex determining gene SRY regulates this process by initiating a pathway of gene and protein expression, including the expression of critical autosomal genes such as SOX9 . (plos.org)
  • This is done through regulation of the activity of proteins that already exist in the cell, but also by the binding of special proteins-transcription factors-to specific sites on the DNA, turning certain genes on or off, which in turn regulates the cell's production of various proteins. (sciencedaily.com)
  • Zinc ion regulates the activities of several enzymes. (dojindo.com)
  • For the most part, companies no longer make or use benzidine, and the government strictly regulates these activities. (cdc.gov)
  • DNA methylation is a chemical process that regulates the function of the genes. (lu.se)
  • The second mode of protection is due to the ability of Dps proteins to bind and oxidize Fe(II) at the characteristic, highly conserved intersubunit ferroxidase center. (wikipedia.org)
  • All MutS proteins also contain a highly-conserved ATP-binding domain and most have weak ATPase activity. (bvsalud.org)
  • An immobilized capture antibody specific for p38 alpha binds both phosphorylated and unphosphorylated p38 alpha. (rndsystems.com)
  • However, molecular weight is also important due to potential steric incompatibilities within protein cores. (hindawi.com)
  • However, it is unclear whether these molecular mechanisms pertain to the entire family of MLL-fusions or if they specifically affect the leukemogenicity of isolated MLL-fusion proteins. (nature.com)
  • Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. (yeastgenome.org)
  • You are expected to delve into the interaction at the molecular level, ideally to describe exactly which amino acid residue(s) of the protein are directly involved in forming the protein-ligand complex, i.e. to explain how the interaction occurs. (usanursingessays.com)
  • Molecular pathogenesis of core binding factor leukemia: current knowledge and future prospects. (medlineplus.gov)
  • Genes can be regarded as blueprints for all of the molecular machines -normally proteins-that perform the tasks an organism needs for survival. (sciencedaily.com)
  • In a paper published in Molecular Cell on July 3 , Young and postdocs Ozgur Oksuz and Jonathan Henninger reveal that along with DNA and protein, many transcription factors can also bind RNA. (mit.edu)
  • It is assumed that the Id helix-loop-helix (HLH) proteins act by associating with ubiquitously expressed basic HLH (bHLH) transcription factors, such as E47 and E2-2, which prevents these factors from forming functional hetero- or homodimeric DNA binding complexes. (lu.se)
  • Several tissue-specific bHLH proteins, including HASH-1, dHAND, and HES-1, are important for development of the nervous system. (lu.se)
  • Cytochrome C, a hemoprotein with peroxidase-like activity when encapsulated inside Dps cage showed better catalytic activity over broad pH range compared to free enzyme in bulk solution. (wikipedia.org)
  • One of the methods that have been proposed is a multiobjective optimization, in which protein stability and catalytic activity are simultaneously optimized [ 4 , 5 ]. (hindawi.com)
  • Several methods have been proposed to design novel stable proteins, such as multi-objective optimization, in which protein stability and catalytic activity are simultaneously optimized. (hindawi.com)
  • Here we describe the 3.2 Å cryo-EM structure of human DEC-205, thereby illuminating the structure of the mannose receptor protein family. (uci.edu)
  • MBL = mannose-binding lectin. (msdmanuals.com)
  • Oxidative stress generated during such stressful conditions may damage DNA and proteins, and as a consequence the cellular processes are disturbed. (springer.com)
  • Our studies have demonstrated that several of the proteins encoded by cellular oncogenes function in fundamental aspects of gene regulation. (stanford.edu)
  • The encoded protein has mitogenic and DNA-binding activity and may play a role in cellular proliferation and differentiation. (thermofisher.com)
  • Single molecule studies have shown that Dps-DNA complexes can get trapped in long-lived metastable states that exhibit hysteresis. (wikipedia.org)
  • Hydroxyl Radical Footprinting of Protein-DNA Complexes Indu Jagannathan and Jeffrey J. Hayes 6. (nhbs.com)
  • Ethylation Interference Footprinting of DNA-Protein Complexes Iain W. Manfield and Peter G. Stockley 10. (nhbs.com)
  • E7 forms complexes with pRb and functionally inactivates pRb and related proteins, such as EF2, which leads to transcription growth-related proteins. (medscape.com)
  • Beyond this protective role, Mrr can inflict chromosomal DNA damage that elicits the SOS response in the host cell upon heterologous expression of specific methyltransferases such as M.HhaII, or after exposure to high pressure (HP). (uci.edu)
  • Mutations in the conserved cysteine residues in the cysteine-rich region led to a decrease in bound iron. (nih.gov)
  • Some mutations delete a few building blocks of DNA (nucleotides) within the TCF4 gene, while other mutations delete the TCF4 gene as well as a number of genes that surround it. (medlineplus.gov)
  • Due to the inherent nature of this plasmid, standard methods to replicate additional amounts of DNA in E. coli are highly likely to result in mutations and/or rearrangements. (origene.com)
  • Spontaneous mutations happen as a result of apparently chance errors in the formation of DNA during cell division. (lu.se)
  • When a cell divides, the mutations are passed on to the daughter cells, but only mutations that occur in the DNA of the gametes are passed on to the next generation. (lu.se)
  • SETD2 loss synergizes with pharmacologic inhibition of the H3K79 methyltransferase DOT1L to induce DNA damage, growth arrest, differentiation, and apoptosis. (nature.com)
  • Different strategies to target hypoxic cancer cells and/or HIFs include hypoxia-activated prodrugs and inhibition of HIF dimerization, mRNA or protein expression, DNA binding capacity, and transcriptional activity. (lu.se)
  • Since an inhibition of telomerase activity may lead to the activation of ALT survivors, potential combinatorial treatments would be a more efficient strategy for cancer therapy. (lu.se)
  • Electromobility shift assays were done to find if proteins from the nucleus bind to the DNA sequence at the TSP. (usda.gov)
  • These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. (embl-heidelberg.de)
  • The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor. (embl-heidelberg.de)
  • The loss of iron led to a approximately 2.5-fold decrease in DNA-binding affinity, indicating that iron was directly involved in SRE1 regulation of iron-uptake genes. (nih.gov)
  • J Virol, 79 2005), a DNA sequence that is responsible for the regulation of estrogen responsive genes in animals. (usda.gov)
  • With the appropriate analysis methods, ChIP-seq can be a valuable approach for elucidating transcription factor binding and cis -level regulation. (ucsc.edu)
  • Depending on the type of mutation, these conditions can be related to impaired regulation of gene activity or loss of normal gene function. (medlineplus.gov)
  • and regulation of DNA-binding transcription factor activity. (nih.gov)
  • Most of this regulation is carried out directly by transcription factors that modulate the activity of promoters aimed at expressing virulence factors. (usp.br)
  • E1 protein has helicase activity for replication, and E2 encodes DNA-binding protein for regulation of transcription. (medscape.com)
  • The ability of Id proteins to affect HES-1 activity is of particular interest in neuronal cells, where regulation of HES-1 is essential for the timing of neuronal differentiation. (lu.se)
  • Here we show that in young proliferating embryonic fibroblasts (MEFs) the Polycomb Repressive Complex 2 (PRC2) member EZH2 together with PRC1 members BMI1 and M33 are strongly expressed and localized at the INK4/ARF regulatory domain (RD) identified as a DNA replication origin. (plos.org)
  • Transcription is regulated through the binding of transcription factor proteins to specific cis -level regulatory sites in the DNA. (ucsc.edu)
  • As DNA methylation is an important regulatory mechanism for gene expression, the identified DNA methylation alterations might contribute to functional changes in the human brain and thereby to the associated behavioral aspects of addiction," first author Eric Poisel, a PhD student at the Central Institute of Mental Health in Mannheim, said in the release. (medscape.com)
  • It is not only the genes that code for proteins that are methylated, but also parts of the DNA that code for regulatory functions (RNA molecules), which can have a greater effect than genes. (lu.se)
  • CHD6 is a DNA-dependent ATPase and localizes at nuclear sites of mRNA synthesis. (nih.gov)
  • The effects of dermatotoxic chemicals on activator protein (AP1) DNA binding activity and c-jun and c-fos messenger RNA (mRNA) levels were examined in normal human epidermal keratinocytes. (cdc.gov)
  • Today we use epigenetics to mean changes to gene expression that are not caused by changes in the actual DNA sequence. (lu.se)
  • Electromobility shift assays showed that the transcription regulator delta-EF1 (dEF1) is one of the proteins that recognize the E box region. (usda.gov)
  • A critical aspect in the control appears to be the recruitment of Rad51 to single-stranded DNA regions exposed as lesions after damage or following a disturbance in DNA synthesis. (cornell.edu)
  • Nucleation was found to be initiated at junctions of double-stranded and single-stranded DNA. (cornell.edu)
  • In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). (rsc.org)
  • Families of related leukemia fusion proteins that share genomic and biological properties represent unique opportunities to study how the combination of distinct functional protein modules can drive oncogenic transformation. (nature.com)
  • Nrf2 consists of six functional Neh domains (Neh1-Neh6), from which, the amino-terminal Neh2 domain controls binding Keap1-the inhibitor protein Kelch-like ECH-associated protein 1, that is responsible for the cytosolic sequestration of Nrf2 under physiological conditions (Fig. 2 a). (springer.com)
  • Biochemists have a much broader definition of the term that can include any other molecule that forms a functional complex with a protein to serve a useful biological role, even if that ligand is large like another macromolecule (eg. (usanursingessays.com)
  • It functions in repair of DNA by homologous recombination by controlling the action of Rad51. (cornell.edu)
  • These findings raise the notion that Brh2 may have roles in homologous recombination beyond the previously established Rad51 mediator activity. (cornell.edu)
  • PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. (springer.com)
  • Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs), generated by SPO11 and accessory proteins (de Massy 2013 ). (springer.com)
  • More recently, his group invented tools for cleavage-free large gene insertion via mining microbial recombination protein, and developed single-cell tracking approach for studying cancer biology and cancer immunology. (stanford.edu)
  • In addition to its role in H3K36 tri-methylation, SETD2 is required to maintain high H3K79 di-methylation and MLL-AF9-binding to critical target genes, such as Hoxa9 . (nature.com)
  • Identification of Protein/DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference Peter E. Shaw and A. Francis Stewart 9. (nhbs.com)
  • Witt and colleagues assessed epigenome-wide DNA methylation signatures of CUD in human postmortem brain tissue of Brodmann area 9 (BA9) in 42 deceased males. (medscape.com)
  • Using patterns of DNA methylation as a measure of the biological age of cells, a total of 20 differentially methylated regions were significantly associated with CUD status after multiple testing correction. (medscape.com)
  • Interestingly, differential DNA methylation was related to several transcription factors and proteins with DNA binding domains, which implies direct effects of these DNA methylation changes on gene expression. (medscape.com)
  • ClpAP seems to play an indirect role in maintaining ongoing dps synthesis during stationary phase Cavities formed by Dps and ferritin proteins have been successfully used as the reaction chamber for the fabrication of metal nanoparticles (NPs). (wikipedia.org)
  • 2004. Decline in transcriptional activity of Nrf2 causes age-related loss of glutathione synthesis, which is reversible with lipoic acid. . (oregonstate.edu)
  • They provide NTPs for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerisation. (embl.de)
  • The IRF5 gene encodes the IRF5 protein that binds to specific regions of DNA and helps control the activity of certain genes. (lupusresearch.org)
  • The discovery of the antioxidant response element (ARE) have led to the conclusion that the battery of genes, including glutamate-cysteine ligase (GCL), thioredoxin reductase 1 (Txnrd1), NAD(P)H-quinone oxidoreductase 1 (NQO1) and heme oxygenase-1 (HMOX1) is regulated through Nrf2 binding to this consensus binding sequence [ 3 ]. (springer.com)
  • Keap1 is a cysteine-rich protein, known to be anchored to actin cytoskeleton [ 5 ], serving as an adaptor protein for the Cul3-dependent E3 ubiquitin ligase complex. (springer.com)
  • A crucial fluorine atom in these inhibitors undergoes SNAr with a cysteine residue in the protein.In this thesis a small library of thirteen compounds and their SAR is reported. (hawaii.edu)
  • VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
  • For instance, the CxxC-domain is essential for DNA binding of MLL-fusion proteins 7 . (nature.com)
  • PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain. (springer.com)
  • In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. (springer.com)
  • Taxonomic distribution of proteins containing NDK domain. (embl.de)
  • The complete taxonomic breakdown of all proteins with NDK domain is also avaliable . (embl.de)
  • Click on the protein counts, or double click on taxonomic names to display all proteins containing NDK domain in the selected taxonomic class. (embl.de)
  • A key characteristic of each transcription factor protein is its DNA binding domain. (ucsc.edu)
  • The reason that researchers had not recognized transcription factors' RNA binding region as such is because it is not a typical RNA binding domain. (mit.edu)
  • In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
  • The task Proteins are the most prevalent macromolecules in biological systems. (usanursingessays.com)
  • For this task you will investigate the interaction between a particular protein and its ligand to learn how the complex formed carries out a useful biological function. (usanursingessays.com)
  • You will research the scientific literature to gather information about the protein, its ligand and the interaction between them, and then use this information to write a 1200-word report on the major features of the protein-ligand complex and its biological function. (usanursingessays.com)
  • The multifunctional regulator nuclear factor erythroid 2-related factor (Nrf2) is considered not only as a cytoprotective factor regulating the expression of genes coding for anti-oxidant, anti-inflammatory and detoxifying proteins, but it is also a powerful modulator of species longevity. (springer.com)
  • Ellagic acid, a compound present in several fruits and medicinal plants, has shown anti-inflammatory activity in several experimental disease models. (hindawi.com)
  • a sugar/carbohydrate, a lipid, another protein, or even a molecule of DNA or RNA). (usanursingessays.com)
  • A protein called p63, which is closely related to another protein that suppresses the formation of tumors, plays an essential role in detecting and responding to DNA damage. (elifesciences.org)
  • Assays showed that multiple proteins can bind to this sequence and that one of these is the transcription regulator delta-EF1 (dEF1). (usda.gov)
  • The 1st identified mobile receptor because of this nuclear proteins was the receptor for advanced glycation end items (Trend), which mediates the relationships between advanced glycation end item (Age group)Cmodified proteins as well as the endothelium and additional cell types (7). (exposed-skin-care.net)
  • Upon senescence, Jmjd3 is overexpressed and the MLL1 protein is recruited to the locus provoking the dissociation of Polycomb from the INK4/ARF locus, its transcriptional activation and its replication during early S-phase. (plos.org)
  • SETD2 loss causes growth arrest and differentiation of AML cells, and leads to increased DNA damage. (nature.com)
  • The TCF4 protein plays a role in the maturation of cells to carry out specific functions (cell differentiation) and the self-destruction of cells (apoptosis). (medlineplus.gov)
  • This change in gene activity blocks the maturation (differentiation) of blood cells and leads to the production of abnormal, immature white blood cells called myeloid blasts. (medlineplus.gov)
  • Modulation of Basic Helix-Loop-Helix Transcription Complex Formation by Id Proteins during Neuronal Differentiation. (lu.se)
  • We found that the three Id proteins expressed in neuroblastoma cells (Id1, Id2, and Id3) were down-regulated during induced differentiation, indicating that Id proteins help keep the tumor cells in an undifferentiated state. (lu.se)
  • After analyzing a set of genes involved in the cell's ability to dispose unneeded proteins in more than 2,500 patients who had come to the NIH with undiagnosed conditions, Dr. Kastner and his team discovered three middle-aged men who suffered from problems such as lung inflammation, skin lesions, and irritated cartilage in the nose and ears. (lupusresearch.org)
  • The difluorocyanobenzenesulfonamide "warhead" that was often included in inhibitors due to its potency, was found to be unstable in plasma due to reaction with native nucleophiles such as glutathione and plasma proteins. (hawaii.edu)
  • OBJECTIVE High-mobility group package-1 (HMGB1) proteins is a nuclear DNA-binding proteins released from necrotic cells, inducing inflammatory reactions and promoting cells restoration and angiogenesis. (exposed-skin-care.net)
  • High-mobility group package-1 (HMGB1) is usually a nuclear proteins that functions as a cytokine when released in to the extracellular milieu by necrotic and inflammatory cells, and it is involved with inflammatory reactions and tissue restoration (4). (exposed-skin-care.net)
  • Mammalian oocytes are arrested in the dictyate stage of meiotic prophase I for long periods of time, during which the high concentration of the p53 family member TAp63α sensitizes them to DNA damage-induced apoptosis. (elifesciences.org)
  • TAp63α is kept in an inactive and exclusively dimeric state but undergoes rapid phosphorylation-induced tetramerization and concomitant activation upon detection of DNA damage. (elifesciences.org)
  • Using a combination of biophysical methods as well as cell and ovary culture experiments we explain how TAp63α is kept inactive in the absence of DNA damage but causes rapid oocyte elimination in response to a few DNA double strand breaks thereby acting as the key quality control factor in maternal reproduction. (elifesciences.org)
  • The protein then switches to an active form when DNA damage is detected to trigger the process of cell self-destruction. (elifesciences.org)
  • This means that once the switch to the active form is triggered there is no delay waiting for other proteins to be made, which makes oocytes extremely sensitive to DNA damage. (elifesciences.org)
  • These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. (rsc.org)
  • also found that the oocytes of mice already contain all the proteins necessary to activate p63. (elifesciences.org)
  • The major characteristics of Nrf2 are to some extent mimicked by Nrf2-dependent genes and their proteins including heme oxygenase-1 (HO-1), which besides removing toxic heme, produces biliverdin, iron ions and carbon monoxide. (springer.com)
  • In the laboratory of David R. Liu at Harvard University, a method has been developed that allows bacteriophages to rapidly evolve DNA-binding proteins autonomously so that they become more targetable over time. (genengnews.com)