• In contrast, other proteins have evolved to bind to specific DNA sequences. (wikipedia.org)
  • Each transcription factor binds to one specific set of DNA sequences and activates or inhibits the transcription of genes that have these sequences near their promoters. (wikipedia.org)
  • 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)
  • 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)
  • 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)
  • For this, we would make use of datasets about containing DNA-binding proteins and the DNA sequences they bind to. (stackexchange.com)
  • 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)
  • 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)
  • Among the proteins that bind to DNA are transcription factors that activate or repress gene expression by binding to DNA motifs and histones that form part of the structure of DNA and bind to it less specifically. (wikipedia.org)
  • 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)
  • Some TF have known binding motifs (very organism dependent), so you'd filter for those with homology to one with a known motifs and go from there -unlikely to give you anything. (stackexchange.com)
  • To mediate its role in chromosome capture, RefZ must bind to specific DNA motifs (RBMs) that localize near the poles at the time of septation. (tamu.edu)
  • The TetR family protein RefZ binds DNA motifs (RBMs) localized near the poles at the time of division and is required for both timely FtsZ assembly and precise capture of DNA in the future spore compartment. (tamu.edu)
  • 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)
  • 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)
  • 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)
  • The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.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)
  • DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract. (wikidata.org)
  • 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)
  • At the cellular level, the actions of glucocorticoids are mediated by a 94-kd protein, the glucocorticoid receptor (GR). The human (h) GR belongs to the steroid/thyroid/retinoic acid superfamily of nuclear receptors and functions as a ligand-dependent transcription factor that regulates the expression of glucocorticoid-responsive genes positively or negatively. (medscape.com)
  • Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. (wikipedia.org)
  • These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence. (wikipedia.org)
  • The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to read the DNA sequence. (wikipedia.org)
  • Protein-DNA interactions occur when a protein binds a molecule of DNA, often to regulate the biological function of DNA, usually the expression of a gene. (wikipedia.org)
  • 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)
  • 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)
  • 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)
  • Deplancke also worked in advanced bioinformatics to derive predictive models for binding interactions. (genomeweb.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)
  • Protein-DNA interactions are essential for many biological processes. (biomedcentral.com)
  • this surface may effect protein-specific interactions. (rcsb.org)
  • 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)
  • 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)
  • Within chromosomes, DNA is held in complexes with structural proteins. (wikipedia.org)
  • We propose that RBM-bound RefZ complexes function as a developmentally regulated nucleoid occlusion system for fine-tuning the position of the septum relative to the chromosome during sporulation.IMPORTANCE The bacterial nucleoid forms a large, highly organized structure. (tamu.edu)
  • In particular, X-ray structures of BEN domain DNA complexes are only known for Drosophila factors bearing a single BEN domain, which lack direct vertebrate orthologs. (bvsalud.org)
  • RFX forms cooperative DNA binding complexes with x2bp and cbf/nf-y. (lu.se)
  • 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)
  • 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)
  • Biophysical studies show that these architectural HMG proteins bind, bend and loop DNA to perform its biological functions. (wikipedia.org)
  • Glass or quartz nanopipettes have found increasing use as tools for studying the biophysical properties of DNA and proteins, and as sensor devices. (imperial.ac.uk)
  • Upon binding, this complex translocates to the cytoplasm, where it interacts with TGF-beta receptor type-1 (TGFBR1), leading to the degradation of both the encoded protein and TGFBR1. (cancerindex.org)
  • In the CYTOPLASM, I-kappa B proteins bind to the transcription factor NF-KAPPA B. Cell stimulation causes its dissociation and translocation of active NF-kappa B to the nucleus. (bvsalud.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)
  • DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. (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)
  • 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)
  • SSB binds with ssDNA with high affinity and low specificity, and is mainly involved in DNA replication, recombination and repair. (biomedcentral.com)
  • This system provides a model for any DNA-binding protein that can be posttranslationally modified to change its affinity for DNA (e.g., through phosphorylation). (ox.ac.uk)
  • However, molecular weight is also important due to potential steric incompatibilities within protein cores. (hindawi.com)
  • 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)
  • 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)
  • 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)
  • 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)
  • Results obtained using electron paramagnetic resonance (EPR), Mössbauer and UV/Visible spectroscopies revealed that Cu 2+ ions bind to specific binding sites in Dps, exerting a rate-enhancing effect on the ferroxidation reaction in the presence of molecular oxygen and directly oxidizing ferrous ions when no other co-substrate is present, in a yet uncharacterized redox reaction. (unl.pt)
  • 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)
  • 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)
  • The RCC1 gene, a regulator for the onset of chromosome condensation was found to encode a protein with a molecular mass of 45 kD, determined using the antibody against the synthetic peptides prepared according to the amino acid sequence of the putative RCC1 protein. (silverchair.com)
  • Mathematical descriptions of protein-DNA binding taking into account sequence-specificity, and competitive and cooperative binding of proteins of different types are usually performed with the help of the lattice models. (wikipedia.org)
  • Computational methods to identify the DNA binding sequence specificity have been proposed to make a good use of the abundant sequence data in the post-genomic era. (wikipedia.org)
  • Understanding the binding specificity of a DNA binding protein is helpful for the research of protein functions. (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)
  • I am a computer scientist and we are working on protein function prediction algorithms. (stackexchange.com)
  • When the ARM binds to HIV RNA, the two molecules form a more stable structure together. (mit.edu)
  • No evidence was obtained for of Chemistry, Lund University water molecules bound with longer residence times. (lu.se)
  • DNA-binding proteins can incorporate such domains as the zinc finger, the helix-turn-helix, and the leucine zipper (among many others) that facilitate binding to nucleic acid. (wikipedia.org)
  • However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
  • Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. (bvsalud.org)
  • Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins . (bvsalud.org)
  • Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins . (bvsalud.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)
  • Several tissue-specific bHLH proteins, including HASH-1, dHAND, and HES-1, are important for development of the nervous system. (lu.se)
  • And even then you may have a somewhat conserved non-coding region or motif, but nothing known because an analogue binds there. (stackexchange.com)
  • Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair. (wikipedia.org)
  • 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)
  • The candidate encoding the longest RBD variant (VB2060) demonstrated high secretion of a functional protein and induced rapid and dose-dependent RBD IgG antibody responses that persisted up to at least 3 months after a single dose of the vaccine in mice. (biorxiv.org)
  • The functional domains and subdomains are indicated beneath the linearized protein structures. (medscape.com)
  • Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. (hindawi.com)
  • There is an urgent need for computational tools that can rapidly and reliably identify DNA-binding sites in DNA-binding proteins. (nature.com)
  • Therefore, a computational method is required to annotate the DNA binding protein as DSB or SSB automatically. (biomedcentral.com)
  • They are typically trained from a set of input features, which can be generally divided into three categories: protein sequence information, protein structure information and a combination of the two categories. (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)
  • Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. (wikidata.org)
  • Is there any software that, given a DNA sequence as input, can predict what protein/ type of protein can bind to the DNA. (stackexchange.com)
  • begingroup$ Given a crystal structure or model of a protein it is incredibly hard predicting the DNA/RNA sequence it binds. (stackexchange.com)
  • How can I predict if the binding site of a DNA-binding protein is located on the promoter sequence of a gene? (stackexchange.com)
  • How can I predict DNA binding affinities from a protein sequence? (stackexchange.com)
  • 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)
  • In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. (bvsalud.org)
  • Scope includes mutations and abnormal protein expression. (cancerindex.org)
  • [ 8 ] Both mutations created stop codons leading to truncation of the PAX3 protein. (medscape.com)
  • These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that form chromosomes. (wikipedia.org)
  • Typical RNA binding domains form stable structures that researchers can detect or predict with current technologies. (mit.edu)
  • Transcription factors do not contain such structures, and so standard searches for RNA binding domains had not identified them in transcription factors. (mit.edu)
  • 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)
  • Specifically, these methods were used to ascertain how the presence of bound Ni2+ ions affects the stability of the known open, cis, and trans forms observed in the crystal structures of this protein as well as their interconversion capability. (sissa.it)
  • 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)
  • The RCC1 protein, a regulator for the onset of chromosome condensation locates in the nucleus and binds to DNA. (silverchair.com)
  • Presumably, RCC1 protein plays a role in regulating the onset of chromosome condensation, at the level of transcription or of mRNA maturation. (silverchair.com)
  • Timely assembly of polar Z rings and precise capture of the chromosome in the forespore both require the DNA-binding protein RefZ. (tamu.edu)
  • During B. subtilis sporulation, the nucleoid undergoes reorganization, and the cell division protein FtsZ assembles polarly to direct septation over one chromosome. (tamu.edu)
  • 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)
  • Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
  • I was looking on Gene Ontology and Protein Databank where I'd expect such informations, but I was unable to find it. (stackexchange.com)
  • 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)
  • The protein encoded by this gene is a nuclear protein that binds the E3 ubiquitin ligase SMURF2. (cancerindex.org)
  • These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription. (wikipedia.org)
  • 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 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)
  • In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
  • The presence of the conserved and tailored Z-DNA-binding surface, which interacts specifically with the zigzag backbone and syn base diagnostic of the Z-form, reinforces the importance to poxvirus infection of the ability of this protein to recognize the Z-conformation. (rcsb.org)
  • In a paper published in Nature Methods this week, a Switzerland-based team of researchers, led by bioengineer Bart Deplancke of the École Polytechnique Fédérale de Lausanne (EPFL), showcased the assay's ability to determine DNA-binding specificities for transcription factors. (genomeweb.com)
  • You are seeking a database of transcription factor binding specificities. (stackexchange.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)
  • 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)
  • 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)
  • The presence of the bound Ni2+ ions does, however, affect significantly the degree of the correlations on the two DNA-binding domains of NikR, which is significantly suppressed as compared to the apo form. (sissa.it)
  • Thus, these proteins are often the targets of the signal transduction processes that control responses to environmental changes or cellular differentiation and development. (wikipedia.org)
  • Tat increases the transcription of HIV's RNA genome by binding to the virus' RNA and then recruiting cellular machinery to it. (mit.edu)
  • Thus, in addition to storing the genetic code, the nucleoid harbors positional information that can be leveraged by DNA-binding proteins to spatially constrain cellular activities. (tamu.edu)
  • Transcription factors are a well-known family of proteins, but new research from Whitehead Institute Member Richard Young and colleagues shows that the picture we have had of them is incomplete. (mit.edu)
  • 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)
  • The DNA contacting surface of Yaba-like disease virus Zalpha(E3L) closely resembles that of other structurally defined members of the Zalpha family, although some variability exists in the beta-hairpin region. (rcsb.org)
  • Here, we characterize several mammalian BEN domain (BD) factors, including from two NACC family BTB-BEN proteins and from BEND3, which has four BDs. (bvsalud.org)
  • This alters the accessibility of the DNA template to the polymerase. (wikipedia.org)
  • Experimental results on 10-fold cross validation indicate that the new feature set are effective to describe DNA binding proteins. (biomedcentral.com)
  • Here, we describe the crystal structure of the Zalpha domain from the E3L-like protein of Yaba-like disease virus, a Yatapoxvirus, in a complex with Z-DNA, solved at a 2.0-A resolution. (rcsb.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)
  • This prompts additional research on the catalytic properties of Dps proteins. (unl.pt)
  • If you do not know the protein, as is your case, homology based methods are the only way. (stackexchange.com)
  • Modulation of Basic Helix-Loop-Helix Transcription Complex Formation by Id Proteins during Neuronal Differentiation. (lu.se)
  • 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)
  • The Smad7 protein is negative regulator of the TGF-β signaling pathway, which is upregulated in patients with breast cancer. (cancerindex.org)
  • 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)
  • The human GR is a modular protein composed of distinct regions illustrated in panel B in the image below, as follows: (1) The amino-terminal A/B region, also called immunogenic or N-terminal domain (NTD) and (2) the C, D, and E regions, which correspond to the DNA-binding domain, the hinge region, and the ligand-binding domain, respectively. (medscape.com)
  • The BEN domain is a recently recognized DNA binding module that is present in diverse metazoans and certain viruses . (bvsalud.org)