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We report here that SRE1, a gene encoding a GATA-type protein, bound to promoter sequences of genes involved in siderophore biosynthesis. (nih.gov)
While DSBs involve in binding to particular dsDNA sequences, to modulate the process of transcription, to cleave DNA molecules, or to be involved in chromosome packaging and transcription in the cell nucleus, etc. (biomedcentral.com)
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)
Some researchers have reported that XNAs containing specific sequences can act as enzymes and bind to proteins. (astrobiology.com)
They also made a longer L-aTNA with a nucleobase sequence that complemented the sequences of the fragments, similar to how DNA strands match up. (astrobiology.com)
Myc proteins are basic helix-loop-helix/ leucine-zipper proteins that bind to specific DNA sequences. (uu.nl)
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)

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
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)
Kornberg 7 has presented that the interactions between DNA and histones are involved in chromosome packaging in the cell nucleus. (nature.com)
Deciphering protein–protein interactions. (crossref.org)
HMGB1 supports transcription of many genes in interactions with many transcription factors. (wikipedia.org)
Selective microfluidics-based ligand enrichment followed by sequencing, or SMiLE-seq, combines antibody arrays, mechanical trapping, and next-generation sequencing readouts to provide a new platform for characterizing DNA-protein interactions. (genomeweb.com)
That year, the two published a paper in Science describing a method to trap low-affinity DNA-protein interactions, specifically those of transcription factors. (genomeweb.com)
By physically restraining bound molecules against an antibody array, they capture both transient interactions, which yeast two-hybrid or tandem mass spectrometry methods don't, and weak interactions, which are usually obliterated by the wash in protein-DNA microarrays. (genomeweb.com)
The transcription factors bind to any number of DNA motifs in the library, those interactions are trapped, and then the readout matches up each motif with the transcription factor via the barcode. (genomeweb.com)
Deplancke also worked in advanced bioinformatics to derive predictive models for binding interactions. (genomeweb.com)
Protein-DNA interactions are essential for many biological processes. (biomedcentral.com)
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)
The article, titled "Dynamic Force Spectroscopy of Protein-DNA Interactions by Unzipping DNA", explains the process of this new technique, which combines two previously known techniques, called dynamic force spectroscopy and unzipping force analysis of protein association, or UFAPA. (cornellsun.com)
In contrast to protein interaction networks, enriched gene ontology (GO) terms of AMI related genes were used to construct a gene ontology interaction (GOI) network, which can be used to simulate the functional interactions between differential expressed genes of disease. (frontiersin.org)
Also, they share a similar protein architecture based on an N-terminal ssDNA binding domain of ~180 amino acids and a C-terminal extension that in the case of RAD52 is required for homologous recombination (HR) through specific protein-protein interactions 6 . (nature.com)
Through its interactions with other proteins via its BRCT domains, hTopBP1 performs diverse functions [ 1 ]. (biomedcentral.com)
The orientation in which MelR binds to site 2' appears to be determined by MelR-MelR interactions rather than by MelR-DNA interactions. (birmingham.ac.uk)
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)
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)

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)
DSBs usually act as transcriptional factors to regulate the genes' expressions, while SSBs usually play roles in DNA replication, recombination, and repair, etc. (biomedcentral.com)
Using DNA microarray chips to analyze the activity of 20,000 genes, the researchers had found numerous genes that were expressed (turned on and off) differently in the brains of depressed people. (nih.gov)
The scientists searched for transcription factors-proteins that bind to the DNA of other genes to turn them on or off-that were capable of regulating the 5 genes. (nih.gov)
Jumonji (JmjC) domain proteins (see Jarid2 ) influence gene expression and chromatin organization by way of histone demethylation, which provides a means to regulate the activity of genes across the genome. (sdbonline.org)
Transcription factors perform this function alone, or with other proteins in a complex, by promoting (as an activator) or blocking (as a repressor) the recruitment of RNA polymerase to specific genes. (horizondiscovery.com)
For a complete list of target genes in this siRNA Library, please contact Technical Support or your local Sales Representative. (horizondiscovery.com)
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)
When transcription factors had their ARMs mutated so they couldn't bind RNA, those transcription factors were less effective in finding their target sites, remaining at those sites and regulating genes. (mit.edu)
The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
Both genes are highly conserved, and their proteins are thought to have 2 functions: (1) formation of a bridge or scaffold between the DNA-binding transcription factors and the RNA polymerase II complex and (2) serving as histone acetyltransferases that open the chromatin structure, a process essential for gene expression. (medscape.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)

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)
Understanding the binding specificity of a DNA binding protein is helpful for the research of protein functions. (biomedcentral.com)
SSB binds with ssDNA with high affinity and low specificity, and is mainly involved in DNA replication, recombination and repair. (biomedcentral.com)
Though there are some researches [ 5 - 7 ] on the SSB and DSB respectively, few attentions have been paid on investigating what makes SSB and DSB have such different kind of binding specificity. (biomedcentral.com)
The great progress of the structure genomics project [ 9 ] results that more and more high resolution 3D structures for DSBs and SSBs are available now, which makes it possible to investigate the common structural differences between SSB and DSB that are responsible for the binding specificity. (biomedcentral.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)
Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. (vu.nl)
Specificity of binding was demonstrated by addition of a 10x excess of non-biotinylated oligo that was able to displace the transcription factor. (qiagen.com)
Interference study of the TDP-43 biosensor using β-amyloid 42 protein and T-tau protein confirmed the specificity of this TDP-43 biosensor. (tmu.edu.tw)

DNA footprinting is the method used to identify the nucleic acid sequence that binds with proteins. (techtarget.com)
After washing, an extraction buffer is added to the nuclei and nucleic acid binding proteins dissociate from DNA and RNA. (qiagen.com)
The Qproteome Nuclear Protein Kit delivers a nucleic acid binding protein fraction suitable for a wide range of activity assays. (qiagen.com)
NX1 extraction buffer (Blank) or 10 µg nucleic acid binding protein fraction was added, washed, and detected colorimetrically in an ELISA procedure using a transcription-factor specific antibody. (qiagen.com)

ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. (cshlpress.com)
We are studying how genome integrity is preserved and the consequences of modifying the program of DNA replication. (umu.se)
Human DNA topoisomerase II-binding protein 1 (hTopBP1) plays an important role in DNA replication and the DNA damage checkpoint pathway. (biomedcentral.com)
During ATR signaling in response to DNA damage, Rad17 forms a complex with 9-1-1 and loads onto stalled replication forks [ 4 - 9 ]. (biomedcentral.com)
Human DNA topoisomerase II-binding protein 1 (TopBP1) and its orthologs play important roles in DNA replication and checkpoint control [ 1 ]. (biomedcentral.com)
The identification of both replication factor C and DNA helicases as critical for sister chromatid pairing has brought new insights into this fundamental process. (rupress.org)
In eukaryotes, DNA replication is separated in time from chromosome segregation. (rupress.org)
For instance, DNA replication and DNA damage checkpoints delay cell cycle progression until each chromosome is fully replicated and physically intact. (rupress.org)
In this article, we reconcile this inconsistency by showing that, in a defined in vitro system with plasmid DNA templates, a variety of sequence-specific DNA-binding proteins, such as the bacteriophage λ O replication initiator or the E. coli lactose or galactose repressors, strikingly stimulate transcription-coupled DNA supercoiling. (johnshopkins.edu)
the processing of the DNA damage replication erro r (Shaughnessy and When DNA damage occurs, the by the cel , which may or may not DeMarini, 2009 ). (who.int)
a cel ular process, frequently invol- tion of DNA damage by an endoge- the DNA damage response includes ving DNA replication. (who.int)

Bacteria often can't support over-expression needed to get workable quantities of protein for an assay, and in vitro expression often can't synthesize a fully functional transcription factor. (genomeweb.com)
In vitro analysis revealed that a putative switch-protein kinase regulator, RsbW, is capable of interacting directly with σ 66 , as well as phosphorylating its own antagonist, RsbV1, rendering it inactive. (plos.org)
We also showed that the presence of an excess of the CTD prevented DNA condensation by ParB and induced disruption of ParB networks in vitro and in vivo. (elifesciences.org)
A simple-prepare, single-use and cost-effective, in vitro biosensor for the detection of TAR DNA-binding protein 43 (TDP-43), a biomarker of neuro-degenerative disorders, was designed, manufactured and tested. (tmu.edu.tw)
Yet, in vitro, clear and convincing support for the twin-domain mechanism has been lacking. (johnshopkins.edu)
No in vitro support and it\'s kind of weak looking so Medium confidence. (utoronto.ca)
1,2 However, recent work has shown that chromatin, the RNA-DNA-protein complex that controls chromosomal organization and gene expression in mammalian nuclei, 3-5 blocks access of Cas9 to certain DNA target sites in vitro 6-8 and in mammalian cells. (aip.org)
8-11 A series of in vitro studies used reconstituted nucleosomes to demonstrate that Cas9/gRNA binding and cleaving are completely blocked at nucleosome-bound DNA. (aip.org)
In vitro synthesis of variola virus DNA exceeding a designated length requires explicit authorization by WHO, as does mutagenesis of orthopoxvirus DNA, larger than a designated length, with the aim of producing the corresponding variola virus sequence. (who.int)

The purpose of this study was to investigate whether an aberrant DNA methylation of transcriptional and inflammatory factors, including TBX21, GATA3, RORγt, FOXP3, IFN-γ, IL-4, IL-17A and TGF-β , in CD4 + T confers risk to BD. (oncotarget.com)
Polycomb Group (PcG) proteins maintain transcriptional repression throughout development, mostly by regulating chromatin structure. (sdbonline.org)
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)
CBP and EP300 are ubiquitously expressed homologous proteins that act as transcriptional co-activators. (medscape.com)

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)
We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein-DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein-DNA complexes containing crystallographically-determined water molecules at their interfaces. (vu.nl)
The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. (vu.nl)
As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein-DNA complexes. (vu.nl)
More precisely, we suggest that some nucleoprotein complexes, perhaps those that contain sharply bent DNA, can form barriers that impede the diffusion and merger of independent chromosomal supercoil domains. (johnshopkins.edu)
Localization of DNA supercoils by nucleoprotein complexes may serve as a general mechanism for modulating DNA transactions that are sensitive to DNA superhelicity. (johnshopkins.edu)
8-11 Recently, several groups have investigated the impact of chromatin states on the binding and cutting of DNA by Cas9 guide RNA complexes (Cas9/gRNA). (aip.org)
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)

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)
Mutations in the conserved cysteine residues in the cysteine-rich region led to a decrease in bound iron. (nih.gov)
When the protein is not acetylated, it stays in the nucleus, but hyperacetylation on lysine residues causes it to translocate into the cytosol. (wikipedia.org)
VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
The MelR derivatives were purified, and the cysteine residues were tagged with p-bromoacetamidobenzyl-EDTA-Fe, an inorganic DNA cleavage reagent. (birmingham.ac.uk)

citation needed] The mechanism of inflammation and damage consists of binding to TLR2 and TLR4, which mediates HMGB1-dependent activation of macrophage cytokine release. (wikipedia.org)
Now that the molecular structure determines its biological function, structural information is expected to provide insight on the binding mechanism of SSB or DSB. (biomedcentral.com)
Thus, in order to research the multi-mechanism complex system in TCM, network pharmacology has been commonly used in recent years to predict the major target proteins or signal pathways of TCM. (frontiersin.org)
By mechanism, DNA annealing proteins are divided into ATPases capable of strand invasion (RecA, RAD51) and single strand annealing proteins (SSAPs) that do not utilize ATP 4 . (nature.com)
These shared biochemical, protein sequence and functional similarities suggest the existence of an ancestral annealing mechanism involved in HR. (nature.com)
The ataxia telangiectasia and Rad3-related protein (ATR) signaling cascade is an important pathway involved in the checkpoint control mechanism [ 3 ]. (biomedcentral.com)
The effectiveness of this bioconjugation mechanism was evaluated and confirmed by FqRRM12 protein, using nuclear magnetic resonance (NMR). (tmu.edu.tw)
Our data are most consistent with a model in which specific DNA-binding proteins facilitate a twin-domain mechanism to enhance DNA supercoiling during transcription. (johnshopkins.edu)

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)
Type I partition systems, also known as ParABS include an ATPase motor protein, ParA, responsible for the movement of the replicated chromosomes to the distal pole of the cell, a DNA binding protein ParB, and a centromere-like DNA sequence, parS ( Funnell, 2016 ). (elifesciences.org)

They are weak ssDNA binding proteins with no affinity for double-stranded (ds) DNA. (nature.com)
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)

As genetics has taken its place on the forefront of scientific technology, this new finding proves especially significant: it is these molecules that allow the information stored on the DNA strands to be translated for use within an organism. (cornellsun.com)

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)
Leng, F & McMacken, R 2002, ' Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins ', Proceedings of the National Academy of Sciences of the United States of America , vol. 99, no. 14, pp. 9139-9144. (johnshopkins.edu)
The Human ON-TARGETplus siRNA Transcription factors Library targets proteins that bind DNA in a sequence-specific manner and thereby control the transfer, or transcription, of genetic information from DNA to RNA. (horizondiscovery.com)
mutant of Max, named dMax, that inhibits sequence-specific DNA binding of Myc proteins. (uu.nl)

cdc2 protein kinase is complexed with both cyclin A and B: Evidence for proteolytic inactivation of MPF. (cshlpress.com)
This study provides evidence that a switch-protein kinase regulatory network controls availability of σ 66 , the main sigma subunit for transcription in Chlamydia . (plos.org)
Giordano G, Sanchez-Perez AM, Montoliu C, Berezney R, Malyavantham K, Costa LG, Calvete JJ, Felipo V. Activation of NMDA receptors induces protein kinase A-mediated phosphorylation and degradation of matrin 3. (medlineplus.gov)
In addition, we investigated several cell cycle-related proteins and found that co-knockdown of hTopBP1 and hMYH significantly diminished cell cycle arrest due to compromised checkpoint kinase 1 (Chk1) activation. (biomedcentral.com)

In terms of predicting where in the genome the transcription factors bind, the models we're able to derive seem to be, in general, actually better than the other assays. (genomeweb.com)
Before genome editing can be used more widely for clinical purposes, researchers need to develop better-targeted DNA-binding proteins. (genengnews.com)
Tat increases the transcription of HIV's RNA genome by binding to the virus' RNA and then recruiting cellular machinery to it. (mit.edu)
CRISPR/Cas9, a DNA-cutting system derived from bacteria, is a popular tool for precise genome engineering. (aip.org)
possibility is that the damage is not induces mutations in a mutation integrated viral genome ( Todaro and repaired at al , and when the cell rep- assay permits it to be classified as Huebner, 1972) , and alteration of im- licates, the DNA polymerase correct- mutagenic. (who.int)

Its active agent is an antibiotic protein called SASP, which binds to bacterial DNA, inactivating it. (growthbusiness.co.uk)
Besides shielding bacterial DNA through binding and condensation, Dps proteins protect the cell from reactive oxygen species by oxidizing and storing ferrous ions within their cavity, using either hydrogen peroxide or molecular oxygen as the co-substrate, thus reducing the toxic effects of Fenton reactions. (unl.pt)

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)
Subunit of the heme-activated, glucose-repressed Hap2/3/4/5 CCAAT-binding complex - there should be a single motif for all four proteins, containing CCAAT. (utoronto.ca)
MITOMI motif 1383 looks like a classic yeast C2H2 binding site (row of G\'s). (utoronto.ca)
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)

It also interacts with nucleosomes to loosen packed DNA and remodel the chromatin. (wikipedia.org)
Moreover, we observed that hMYH was essential for the accumulation of hTopBP1 on damaged DNA, where hTopBP1 interacts with hRad9, a component of the Rad9-Hus1-Rad1 complex. (biomedcentral.com)
It interacts also with anticoagulant protein S and with serum amyloid P component. (lu.se)

Some studies indicate that matrin 3 binds and stabilizes a type of RNA called messenger RNA (mRNA), which provides the genetic blueprint for proteins. (medlineplus.gov)
This suggests that genetic code could be transferred from DNA and RNA onto L-aTNA and vice versa. (astrobiology.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 are two kinds of DNAs, single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). (biomedcentral.com)

Like the histones, HMGB1 is among the most important chromatin proteins. (wikipedia.org)
HMGB1 is a nuclear protein that binds to DNA and acts as an architectural chromatin-binding factor. (wikipedia.org)
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)
The accumulation of hTopBP1 on chromatin and its subsequent interaction with hRad9 lead to cell cycle arrest, a process mediated by Chk1 phosphorylation and ataxia telangiectasia and Rad3-related protein (ATR) activation. (biomedcentral.com)
We also tested DNA-binding, transiently expressed activation-associated proteins (AAPs) that are known to support an open, transcriptionally active chromatin state. (aip.org)
Our results demonstrate the use of DNA-binding, activator-associated fusion proteins as an effective method to enhance Cas9 editing within polycomb-repressed chromatin. (aip.org)

One possibility is that the CTD simply competes for the binding sites in the DNA molecule ( Figure 1B , DNA-binding competition model). (elifesciences.org)
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)
a sugar/carbohydrate, a lipid, another protein, or even a molecule of DNA or RNA). (usanursingessays.com)
Examples DNA repair and apoptosis path- concept is that there is a distinct dif- of DNA damage are DNA adducts ways, which are described in detail ference between DNA damage and (i.e. a molecule bound covalently to by Ciccia and El edge (2010) . (who.int)

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)

Nagoya University scientists in Japan have demonstrated how DNA-like molecules could have come together as a precursor to the origins of life. (astrobiology.com)
When the ARM binds to HIV RNA, the two molecules form a more stable structure together. (mit.edu)

CHD6 is a DNA-dependent ATPase and localizes at nuclear sites of mRNA synthesis. (nih.gov)
Our results suggest that an aberrant DNA methylation of GATA3 and TGF-β is associated with their mRNA expression and participates in the pathogenesis of BD. (oncotarget.com)

In a mouse model of SCA1, mutant ataxin 1 protein mediated the reduction or inhibition of HMGB1 in the mitochondria of neurons. (wikipedia.org)
It also decreased the number of connections between neurons, supporting the idea that higher Gata1 expression can lead to the changes seen in depressed brains. (nih.gov)

As evaluated by co-immunoprecipitation experiments, the dsDNA recombination function relates to the Redα-Redβ protein-protein interaction, which requires not only contacts in the C-terminal domain but also a region near the N-terminus. (nature.com)
RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data. (tartaglialab.com)
Our results suggested that hMYH is necessary for the accumulation of hTopBP1 to DNA damage lesion to induce the association of hTopBP1 with 9-1-1 and that the interaction between hMYH and hTopBP1 is essential for Chk1 activation. (biomedcentral.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 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)
You are free to investigate a protein-ligand interaction of your own choosing and that you find interesting. (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)

Binding of the Escherichia coli MelR protein to the melAB promoter: orientation of MelR subunits and investigation of MelR-DNA contacts. (birmingham.ac.uk)
The Escherichia coli MelR protein is a melibiose-triggered transcription factor, belonging to the AraC family, that activates transcription initiation at the melAB promoter. (birmingham.ac.uk)
Transcription by RNA polymerase can stimulate localized DNA supercoiling in Escherichia coli. (johnshopkins.edu)
The recent Encyclopedia of studies in the 1950s and 1960s in Escherichia coli and then by DNA Elements (ENCODE) project showed binding of carcinogens to nu- Szybalski (1958) , who tested more indicates that at least 80% of the cleic acids ( Wiest and Heidelberger, than 400 compounds in E. coli . (who.int)

In adipocytes, the sterol regulatory element binding protein pathway is increased, resulting in increases in levels of sterol regulatory element binding protein 1 and fatty acid synthase. (cdc.gov)

HMGB1-LPS complex activates TLR4, and causes the binding of adapter proteins (MyD88 and others), leading to signal transduction and the activation of various signaling cascades. (wikipedia.org)
We studied CTP- and parS F -modulated ParA F -ParB F complex assembly, in which DNA-bound ParA F -ATP dimers are activated for ATP hydrolysis by interacting with two ParB F N-terminal domains. (biorxiv.org)
Magnetic-tweezers experiments showed that CTP promotes multiple ParB F loading onto parS F -containing DNA, generating condensed partition complex-like assemblies. (biorxiv.org)
and results in the formation of a large nucleo-protein complex (the partition complex) around the parS site on the DNA to be partitioned. (biorxiv.org)
Solvated docking leads to an overall improvement in the quality of the generated protein-DNA models for cases with limited conformational change of the partners upon complex formation. (vu.nl)
In vivo, there is extensive experimental support for a "twin-domain" model in which positive DNA supercoils are generated ahead of a translocating RNA polymerase complex and negative supercoils are formed behind it. (johnshopkins.edu)
These data support the hypothesis that N-Myc affects neuroblastoma gene expression through the formation of a DNA-binding heterodimeric complex with Max in vivo. (uu.nl)
Modulation of Basic Helix-Loop-Helix Transcription Complex Formation by Id Proteins during Neuronal Differentiation. (lu.se)
However, the Id proteins did complex with HES-1, and increased levels of Id2 reduced the DNA binding activity of HES-1. (lu.se)

For instance, SMC proteins (COOH-terminal fragments) are capable of binding DNA in the absence of Mcd1p. (rupress.org)
The team also demonstrated that L-aTNA fragments could interlink on DNA and RNA templates. (astrobiology.com)
The Committee recommended extending permissible distribution of variola virus DNA to include chips containing minute amounts of multiple short fragments of variola virus DNA, irreversibly bound to a solid support. (who.int)
Attempts to synthesize full-length variola virus genomes or infectious variola viruses from smaller DNA fragments remain strictly prohibited. (who.int)

In turn, Mcd1p requires SMC proteins and Pds5p requires Mcd1p for chromosomal recruitment. (rupress.org)

Several tissue-specific bHLH proteins, including HASH-1, dHAND, and HES-1, are important for development of the nervous system. (lu.se)

As opposed to single strand (ss) DNA binding proteins such as SSB and RPA, which protect and occlude ssDNA from recombination, RAD52/Redβ SSAPs promote recombination and share several biochemical similarities. (nature.com)
Both crystal structures revealed that the N-terminal domain of ~200 amino acids forms a mushroom-shaped undecameric ring with an external groove lined with positive charges, which probably binds the phosphodiester backbone of ssDNA. (nature.com)

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)
In the meantime, the investigation results can help to annotate or refine the annotation of the proteins with known structures yet unknown or not fully understood functions. (biomedcentral.com)

I. Separation of the strands of SV40 DNA and hybridization of the separated strands to RNA extracted from lytically infected and transformed cells. (cshlpress.com)
Single strand annealing proteins (SSAPs) like Redβ initiate homologous recombination by annealing complementary DNA strands. (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)
Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. (hindawi.com)

The assay could help accelerate efforts to map where transcription factors bind the genomes of humans and model organisms, Deplancke said. (genomeweb.com)

One of the oxidative DNA lesions frequently generated upon exposure of cells to reactive oxygen species (ROS) is 7,8-dihydro-8-oxoguanine (8-oxoG) [ 13 ]. (biomedcentral.com)

However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
The nuclear matrix is a network of proteins that provides structural support for the nucleus and aids in several important nuclear functions. (medlineplus.gov)

Dps proteins (DNA-binding proteins from starved cells) are multifunctional stress defense proteins from the Ferritin family expressed in Prokarya during starvation and/or acute oxidative stress. (unl.pt)

Because levels of transcription factor CCAAT/enhancer binding protein-β, peroxisome proliferator-activated receptor-γ, and lipoprotein lipase are also increased, lipid transport into cells and fatty acid synthesis within cells is increased ( 8 - 15 ). (cdc.gov)

Add 1 pg-100 ng of plasmid DNA (1-5 µl) to cells and mix without vortexing. (neb.com)

Alternatively, a stepwise assembly model positing that subunits are sequentially recruited is gaining biochemical support ( Skibbens, 2000 ). (rupress.org)
In this work, we have studied the binding of MelR to different sites at the melAB promoter, focusing on the orientation of binding of the two MelR HTH motifs, and the juxtaposition of the different bound MelR subunits with respect to each other. (birmingham.ac.uk)
The activity of CDKs is controlled by their binding to coactivator subunits termed Cyclins, as well as by CDK inhibitory proteins termed CKIs. (intechopen.com)

We demonstrate further that this stimulation requires the presence in the DNA template of a recognition sequence for the relevant DNA-binding protein and depends on the production of long RNA chains by an RNA polymerase. (johnshopkins.edu)

Bacillus subtilis ParB forms multimeric networks involving non-specific DNA binding leading to DNA condensation. (elifesciences.org)
Previously, we found that an excess of the free C-terminal domain (CTD) of ParB impeded DNA condensation or promoted decondensation of pre-assembled networks (Fisher et al. (elifesciences.org)
2017). However, interpretation of the molecular basis for this phenomenon was complicated by our inability to uncouple protein binding from DNA condensation. (elifesciences.org)
Here, we have combined lateral magnetic tweezers with TIRF microscopy to simultaneously control the restrictive force against condensation and to visualise ParB protein binding by fluorescence. (elifesciences.org)
At non-permissive forces for condensation, ParB binds non-specifically and highly dynamically to DNA. (elifesciences.org)
we studied the role of the C-terminal domain (CTD) of ParB in its multimerisation and DNA condensation. (elifesciences.org)
In particular, we confirmed its dimeric stoichiometry and identified a novel intermolecular non-specific DNA-binding site across the positively-charged β-sheet face of the CTD of ParB, which was critical for DNA condensation. (elifesciences.org)

High mobility group box 1 protein, also known as high-mobility group protein 1 (HMG-1) and amphoterin, is a protein that in humans is encoded by the HMGB1 gene. (wikipedia.org)

exposed side chains, and weak ligand binding. (lu.se)

We were able to synthesize an XNA without enzymes, strongly supporting the hypothesis that an XNA world might have existed before the RNA world. (astrobiology.com)

For studies on cytokine production, cells are first treated with a protein transport inhibitor to allow accumulation of the target protein inside the cell. (bdbiosciences.com)
The accumulation of both Cyclin and CKI proteins is tightly regulated at the level of transcription. (intechopen.com)

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)

This nuclear protein organizes the DNA and regulates transcription. (wikipedia.org)
The Qproteome Nuclear Protein Kit is intended for molecular biology applications. (qiagen.com)
The Qproteome Nuclear Protein Kit is designed for specific enrichment of nuclear proteins from cultured mammalian cells. (qiagen.com)

In order to simplify our analysis, we exploited an engineered derivative of the melAB promoter in which MelR binding to site 2 and site 2', in the absence of CRP, is sufficient for transcription activation. (birmingham.ac.uk)
Our results show that MelR binds as a direct repeat to site 2 and site 2' with the C-terminal HTH located towards the promoter-proximal end of each site. (birmingham.ac.uk)

All members of the AraC family contain two helix-turn-helix (HTH) motifs that contact two segments of the DNA major groove at target sites on the same DNA face. (birmingham.ac.uk)
Patterns of DNA cleavage after MelR binding were then used to determine the positions of the two HTH motifs at target sites. (birmingham.ac.uk)
Also resembles motifs obtained by both ChIP and PBMs for related protein Nrg1. (utoronto.ca)

Negative supercoils accumulate in the template DNA because the positive supercoils are preferentially removed by cellular topoisomerase action. (johnshopkins.edu)

In addition, Cyclin and CKI proteins are controlled at the level of their destruction. (intechopen.com)

This mutation, known as Ser85Cys (or S85C), replaces the amino acid serine with the amino acid cysteine at position 85 of the protein. (medlineplus.gov)

Anatomy13

Organisms22

Diseases1

Chemicals and Drugs119

Analytical, Diagnostic and Therapeutic Techniques and Equipment28

Phenomena and Processes74

Technology, Industry, Agriculture1

Information Science4

Health Care2

Sequences9

Interactions19

Genes12

Specificity13

Nucleic acid4

Replication11

Vitro9

Transcriptional4

Complexes8

Residues6

Mechanism8

Centromere-like DNA sequence2

Affinity2

Genetics1

Sequence-specific4

Kinase4

Genome5

Bacterial2

Motif4

Interacts3

Genetic2

DNAs2

Chromatin7

Molecule4

Phosphorylation2

Molecules2

MRNA2

Neurons2

Interaction7

Escherichia4

Pathway1

Complex9

Fragments4

Chromosomal1

BHLH1

SsDNA2

Annotation2

Strands2

Computational2

Transcription factors bind1

Reactive oxygen1

Structural2

Oxidative1

CCAAT1

Plasmid1

Subunits3

Polymerase1

Condensation7

Humans1

Ligand1

Enzymes1

Accumulation2

Neuroblastoma1

Nuclear protein3

Promoter2

Motifs3

Topoisomerase1

Cyclin1

Cysteine1