• The CHD7 gene provides instructions for making a protein called chromodomain helicase DNA binding protein 7. (medlineplus.gov)
  • 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)
  • 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)
  • DNA sequences encoding cardiac myosin-binding protein C were determined in unrelated patients with familial hypertrophic cardiomyopathy. (nih.gov)
  • For this, we would make use of datasets about containing DNA-binding proteins and the DNA sequences they bind to. (stackexchange.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)
  • Kornberg 7 has presented that the interactions between DNA and histones are involved in chromosome packaging in the cell nucleus. (nature.com)
  • Possible DNA-binding interactions are discussed on the basis of comparisons to other winged helix proteins. (rcsb.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)
  • 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)
  • Deciphering protein–protein interactions. (crossref.org)
  • Unveil the DNA forms and delve into the major and minor grooves that play roles in protein-DNA interactions, gene regulation, and more. (thesciencenotes.com)
  • Adenovirus protein- protein interactions: hexon and protein VI. (microbiologyresearch.org)
  • 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)
  • 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)
  • Survival was generally better than that observed among patients with hypertrophic cardiomyopathy caused by other mutations in the genes for sarcomere proteins. (nih.gov)
  • Most unexpectedly, genes coding for similar proteins were found in the genomes of eukaryotes, including humans. (johnshopkins.edu)
  • Researchers are working to determine which genes the CHD7 protein regulates. (medlineplus.gov)
  • Biophysical studies show that these architectural HMG proteins bind, bend and loop DNA to perform its biological functions. (wikipedia.org)
  • Biophysical studies showed that the orthologs of the two OB fold/one zinc finger replication protein A in Hethanosarcina acetivorans and Methanopyrus kandleri exhibit two binding modes, wrapping and stretching of DNA. (johnshopkins.edu)
  • 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)
  • DNA-binding proteins include transcription factors which modulate the process of transcription, various polymerases, nucleases which cleave DNA molecules, and histones which are involved in chromosome packaging and transcription in the cell nucleus. (wikipedia.org)
  • Timely assembly of polar Z rings and precise capture of the chromosome in the forespore both require the DNA-binding protein RefZ. (tamu.edu)
  • 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)
  • 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)
  • During B. subtilis sporulation, the nucleoid undergoes reorganization, and the cell division protein FtsZ assembles polarly to direct septation over one chromosome. (tamu.edu)
  • And now, scientists have discovered how Dsup binds to chromosome structures and protects DNA from the harmful effects of radiation, the researchers reported in a new study. (livescience.com)
  • 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)
  • 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)
  • 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)
  • We created several deletion mutants of this protein based on its conserved motifs, and from these structures functional chimeras were synthesized, supporting the hypothesis that gene duplication and recombination could lead to novel functional forms of single-stranded DNA-binding proteins. (johnshopkins.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)
  • abstract = "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)
  • Most interestingly, a second single-stranded DNA-binding protein, FacRPA2, in this archaeon exhibited the wrapping mode. (johnshopkins.edu)
  • 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)
  • 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)
  • 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)
  • 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)
  • The protective protein binds to cell structures that contain DNA. (livescience.com)
  • Results: We present ZEAL, an interactive tool to superpose global and local protein structures based on their shape resemblance using 3D (Zernike-Canterakis) functions to represent the molecular surface. (lu.se)
  • The telomeres are the DNA-protein structures at the ends of eukaryotic chromosomes, which serve to protect and stabilize the genome. (lu.se)
  • In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
  • Superposition of proteins based on surface shape can enable comparison of highly divergent proteins, identify convergent evolution and enable detailed comparison of surface features and binding sites. (lu.se)
  • I am a computer scientist and we are working on protein function prediction algorithms. (stackexchange.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 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)
  • 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)
  • Mutations in the gene for cardiac myosin-binding protein C account for approximately 15 percent of cases of familial hypertrophic cardiomyopathy. (nih.gov)
  • The genotypes of these family members were determined, and the clinical status of 212 family members with mutations in the gene for cardiac myosin-binding protein C was assessed. (nih.gov)
  • eight defects (insertions, deletions, and splice mutations) were predicted to truncate cardiac myosin-binding protein C. The clinical expression of either missense or truncation mutations was similar to that observed for other genetic causes of hypertrophic cardiomyopathy, but the age at onset of the disease differed markedly. (nih.gov)
  • The clinical expression of mutations in the gene for cardiac myosin-binding protein C is often delayed until middle age or old age. (nih.gov)
  • Delayed expression of cardiac hypertrophy and a favorable clinical course may hinder recognition of the heritable nature of mutations in the cardiac myosin-binding protein C gene. (nih.gov)
  • Most of these mutations lead to the production of an abnormal CHD7 protein that is broken down prematurely. (medlineplus.gov)
  • Most of the CHD7 gene mutations that cause Kallmann syndrome alter single protein building blocks (amino acids) in the CHD7 protein. (medlineplus.gov)
  • Studies suggest that these mutations have a less severe effect on protein function than those that cause CHARGE syndrome. (medlineplus.gov)
  • Scope includes mutations and abnormal protein expression. (cancerindex.org)
  • VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.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)
  • The MelR derivatives were purified, and the cysteine residues were tagged with p-bromoacetamidobenzyl-EDTA-Fe, an inorganic DNA cleavage reagent. (birmingham.ac.uk)
  • In prokaryotes, multiple types of proteins are involved. (wikipedia.org)
  • By piecing together how Dsup functions at ever-more-precise levels, scientists can then use it as a blueprint for building other types of proteins - "better versions of Dsup" - that are even more effective at protecting cells from DNA damage, Kadonaga said. (livescience.com)
  • 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)
  • 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)
  • However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
  • It shares homology with the mating-type protein, Mc, from the fission yeast Schizosaccharomyces pombe and a conserved DNA-binding motif present in the nuclear high-mobility-group proteins HMG1 and HMG2. (nih.gov)
  • 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)
  • A protein found only in tardigrades provides cellular DNA with a unique form of protection. (livescience.com)
  • We thought this fascinating protein in an extreme organism might tell us something new that we wouldn't get from regular proteins," said study co-author James Kadonaga, a professor with the Division of Biological Sciences at the University of California, San Diego. (livescience.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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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 architecture of single-stranded DNA-binding proteins, which play key roles in DNA metabolism, is based on different combinations of the oligonucleotide/oligosaccharide binding (OB) fold. (johnshopkins.edu)
  • We therefore focus on elucidating the roles of the telomere binding proteins in this process. (lu.se)
  • 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)
  • hi, I try to purify a protein from yeast to assay some structural studies. (bio.net)
  • 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)
  • 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)
  • Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.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)
  • 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)
  • CHD6 is a DNA-dependent ATPase and localizes at nuclear sites of mRNA synthesis. (nih.gov)
  • The protein encoded by this gene is a nuclear protein that binds the E3 ubiquitin ligase SMURF2. (cancerindex.org)
  • 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)
  • These agents are characterized by their ability to bind covalently to nucleophilic sites in proteins and DNA. (cdc.gov)
  • 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)