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  • domain
  • The binding of zinc (II) in the CCHC binding site is necessary for the domain to be functional and for the stabilization of the conformation of the structure, allowing the NCp7 to carry out the processes required for HIV replication. (wikipedia.org)
  • site
  • Since the CCHC binding site is mutation resistant and involved in the replication of HIV-1, it makes a prime candidate for the prevention of HIV through zinc ejectors. (wikipedia.org)
  • This electrophilic interaction destabilizes the zinc binding site making it easier for the zinc ion to be withdrawn due to the new arrangement of bonds. (wikipedia.org)
  • The binding site then performs a disulfide exchange, forming new intermolecular disulfide bonds, and rearrangement occurs placing the zinc finger in a conformation that inhibits its function. (wikipedia.org)
  • If the zinc finger domains perfectly recognize a 3 basepair DNA sequence to generate a 3-finger array that can recognize a 9 basepair target site. (wikipedia.org)
  • specific
  • Evolutionary success of natural zinc finger proteins, however, evinces that nature created specific evolutionary traits and strategies, such as modularity and rank-specific recognition to cope with binding complexity that are critical for creating clinical viable tools to precisely modify the human genome. (osti.gov)
  • vitro
  • The results are very poor (about 1% with 35S in vitro synthetized proteins). (bio.net)
  • There have been a wide variety of experimental methods such as in vitro methods [ 4 , 5 ] like filter binding assays, chromatin immunoprecipitation on microarrays (ChIP-chip) genetic analysis, and X-ray crystallography which are used to predict DNA-binding proteins. (hindawi.com)
  • For example, the (SSB)65 binding mode, in which approximately 65 nucleotides of DNA wrap around the SSB tetramer and contact all four of its subunits, is favoured at high salt concentrations in vitro. (wikipedia.org)
  • Dps dodecamers can condense DNA in vitro through a cooperative binding mechanism. (wikipedia.org)
  • Gel shift assays are often performed in vitro concurrently with DNase footprinting, primer extension, and promoter-probe experiments when studying transcription initiation, DNA replication, DNA repair or RNA processing and maturation, as well as pre-mRNA splicing. (wikipedia.org)
  • Once DNA-protein binding is determined in vitro, a number of algorithms can narrow the search for identification of the transcription factor. (wikipedia.org)
  • The in vitro model, which is a very well known method of facilitated diffusion, that takes place outside of a living cell, explains the 3-dimensional pattern of diffusion in the cytosol and the 1-dimensional diffusion along the DNA contour. (wikipedia.org)
  • After analyzing the process for the time it takes for TF's to diffuse across the contour and cytoplasm of the bacteria's DNA, it was concluded that in vitro and in vivo are similar in that the association and dissociation rates of TF's to and from the DNA are similar in both. (wikipedia.org)
  • residues
  • In molecular biology, bacterial DNA binding proteins are a family of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins. (wikipedia.org)
  • This protein domain has a conserved region of around 80 residues. (wikipedia.org)
  • Three consecutive amino acid residues form an anion-binding concavity. (wikipedia.org)
  • Three or four consecutive amino acid residues form a cation-binding feature. (wikipedia.org)
  • The ARID2 protein contains two conserved C-terminal C2H2 zinc fingers motifs, a region rich in the amino acid residues proline and glutamine, a RFX (regulatory factor X)-type winged-helix DNA-binding domain, and a conserved N-terminal AT-rich DNA interaction domain-the last domain for which the protein is named. (wikipedia.org)
  • 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)
  • viral
  • Participates in the detection by the host's innate immune system of DNA from viral, bacterial or even host origin. (uniprot.org)
  • bacterial
  • Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. (nih.gov)
  • Since bacterial binding proteins have a diversity of functions, it has been difficult to develop a common function for all of them. (wikipedia.org)
  • Upon further investigation, it was discovered that the amino acid composition of HU resembles that of eukaryotic histones, thus prompting further research into the exact function of bacterial DNA binding proteins and discoveries of other related proteins in bacteria. (wikipedia.org)
  • HU is a small (10 kDa) bacterial histone-like protein that resembles the eukaryotic Histone H2B. (wikipedia.org)
  • DPS proteins are part of a complex bacterial defence system that protects DNA against oxidative damage and are distributed widely in the bacterial kingdom. (wikipedia.org)
  • posttranslational modifications
  • The Eastern blot is used for the detection of specific posttranslational modifications of proteins. (wikipedia.org)
  • Proteins are separated by gel electrophoresis before being transferred to a blotting matrix whereupon posttranslational modifications are detected by specific substrates (cholera toxin, concanavalin, phosphomolybdate, etc.) or antibodies. (wikipedia.org)
  • identical
  • DPS are highly symmetrical dodecameric proteins of 200 kDa characterized from a shell-like structure of 2:3 tetrahedral symmetry assembled from identical subunits with an external diameter of ~ 9 nm and a central cavity of ~ 4.5 nm in diameter. (wikipedia.org)
  • nucleus
  • Eukaryotic histones package DNA to help it to fit in the nucleus, and they are known to be the most conserved proteins in nature. (wikipedia.org)
  • When cells are exposed to UV radiation, DDB1 moves from the cytosol to the nucleus and binds to DDB2, thus forming the UV-DDB complex. (wikipedia.org)
  • biological
  • p>This section provides any useful information about the protein, mostly biological knowledge. (uniprot.org)
  • Motifs do not allow us to predict the biological functions: they are found in proteins and enzymes with dissimilar functions. (wikipedia.org)
  • subunits
  • At lower salt concentrations, the (SSB)35 binding mode, in which about 35 nucleotides bind to only two of the SSB subunits, tends to form. (wikipedia.org)
  • This complex is composed of two protein subunits, a large subunit DDB1 (p127) and a small subunit DDB2 (p48). (wikipedia.org)
  • targets
  • 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)
  • ID proteins could be potential targets for systemic cancer therapies without inhibiting the functioning of most normal cells because they are highly expressed in embryonic stem cells, but not in differentiated adult cells. (wikipedia.org)
  • Also, on the DNA contour, the motion is slower and target sites are easy to localize while in the cytoplasm, the motion is faster but the TF's are not sensitive to their targets and so binding is restricted. (wikipedia.org)
  • structural
  • The individual A and B boxes (which, although broadly similar, show both structural and functional differences) exhibit many of the structure-specific properties of the whole protein. (biochemsoctrans.org)
  • Within chromosomes, DNA is held in complexes with structural proteins. (wikipedia.org)
  • When H-NS is bound with RNA Polymerase to the promoter region, there are structural differences in the DNA that are accessible. (wikipedia.org)
  • In proteins, a structural motif describes the connectivity between secondary structural elements. (wikipedia.org)
  • In addition to secondary structural elements, protein structural motifs often include loops of variable length and unspecified structure. (wikipedia.org)
  • Sequence motif Short linear motif PROSITE Database of protein families and domains SCOP Structural classification of Proteins CATH Class Architecture Topology Homology FSSP FSSP PASS2 PASS2 - Protein Alignments as Structural Superfamilies SMoS SMoS - Database of Structural Motifs of Superfamily S4 S4: Server for Super-Secondary Structure Motif Mining Chiang YS, Gelfand TI, Kister AE, Gelfand IM (2007). (wikipedia.org)
  • coli
  • In E. coli, H-NS binds to a P1 promoter decreasing rRNA production during stationary and slow growth periods. (wikipedia.org)
  • In prokaryotic bacteria cells such as E. coli, facilitated diffusion is required in order for regulatory proteins to locate and bind to target sites on DNA base pairs. (wikipedia.org)
  • cellular
  • There were several control experiments and additional experiments showing that the presence of other cellular proteins on the DNA didn't have much of an effect. (blogspot.com)
  • Fragment
  • The control lane (DNA probe without protein present) will contain a single band corresponding to the unbound DNA or RNA fragment. (wikipedia.org)
  • However, assuming that the protein is capable of binding to the fragment, the lane with protein present will contain another band that represents the larger, less mobile complex of nucleic acid probe bound to protein which is 'shifted' up on the gel (since it has moved more slowly). (wikipedia.org)
  • When using a biotin label, streptavidin conjugated to an enzyme such as horseradish peroxidase is used to detect the DNA fragment. (wikipedia.org)
  • Southern blotting combines transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detection by probe hybridization. (wikipedia.org)
  • UniProt
  • p>When browsing through different UniProt proteins, you can use the 'basket' to save them, so that you can back to find or analyse them later. (uniprot.org)
  • mRNA
  • It has also been found that H-NS can affect translation as well by binding to mRNA and causing its degradation. (wikipedia.org)
  • locates
  • There are 2 main steps involved: the protein binds to a non-specific site on the DNA and then it diffuses along the DNA chain until it locates a target site, a process referred to as sliding. (wikipedia.org)
  • domain
  • The binding of zinc (II) in the CCHC binding site is necessary for the domain to be functional and for the stabilization of the conformation of the structure, allowing the NCp7 to carry out the processes required for HIV replication. (wikipedia.org)
  • site
  • Since the CCHC binding site is mutation resistant and involved in the replication of HIV-1, it makes a prime candidate for the prevention of HIV through zinc ejectors. (wikipedia.org)
  • This electrophilic interaction destabilizes the zinc binding site making it easier for the zinc ion to be withdrawn due to the new arrangement of bonds. (wikipedia.org)
  • The binding site then performs a disulfide exchange, forming new intermolecular disulfide bonds, and rearrangement occurs placing the zinc finger in a conformation that inhibits its function. (wikipedia.org)
  • If the zinc finger domains perfectly recognize a 3 basepair DNA sequence to generate a 3-finger array that can recognize a 9 basepair target site. (wikipedia.org)
  • specific
  • Evolutionary success of natural zinc finger proteins, however, evinces that nature created specific evolutionary traits and strategies, such as modularity and rank-specific recognition to cope with binding complexity that are critical for creating clinical viable tools to precisely modify the human genome. (osti.gov)
  • Genes
  • Later in the 2000's, post-genomic research in his laboratory established signature proteins in halophilic Archaea, and the function of many genes and genetic elements, including multiple replication origins, general transcription factors, and DNA repair systems. (wikipedia.org)
  • These vesicles are complex structures made of proteins encoded by at least 14 genes. (wikipedia.org)
  • however it is highly homologous to other LILR genes, and can bind human leukocyte antigen (HLA) class I. Therefore, if secreted, the LILRA3 might impair interactions of membrane-bound LILRs (such as LILRB1, an inhibitory receptor expressed on effector and memory CD8 T cells) with their HLA ligands, thus modulating immune reactions and influencing susceptibility to disease. (wikipedia.org)
  • degradation
  • Ubiquitin is a small protein in all living organisms that "marks" other proteins for degradation or, as more recently discovered, the participation in specific cellular processes such as recombination. (medicalxpress.com)
  • The apoptotic process is accompanied by shrinkage and fragmentation of the cells and nuclei and degradation of the chromosomal DNA into nucleosomal units. (wikipedia.org)
  • These proteolytic active sites located in the inner side of a chamber formed by 4 stacked rings of 20S subunits, preventing random protein-enzyme encounter and uncontrolled protein degradation. (wikipedia.org)
  • The 19S regulatory particles can recognize ubiquitin-labeled protein as degradation substrate, unfold the protein to linear, open the gate of 20S core particle, and guide the substate into the proteolytic chamber. (wikipedia.org)
  • antigen
  • The carcinoembryonic antigen (CEA), a protein involved in cell adhesion, is a biomarker of colorectal cancer and, if present in the blood, is an indication that the disease is present. (nanowerk.com)
  • Leukocyte immunoglobulin-like receptor subfamily A member 3 (LILR-A3) also known as CD85 antigen-like family member E (CD85e), immunoglobulin-like transcript 6 (ILT-6), and leukocyte immunoglobulin-like receptor 4 (LIR-4) is a protein that in humans is encoded by the LILRA3 gene located within the eukocyte receptor complex on chromosome 19q13.4. (wikipedia.org)
  • fragment
  • Decomp - Suppose you are given a DNA fragment of mass 1897.27 Dalton and no other information. (uni-bielefeld.de)
  • If a "phagemid" vector is used (a simplified display construct vector) phage particles will not be released from the E. coli cells until they are infected with helper phage, which enables packaging of the phage DNA and assembly of the mature virions with the relevant protein fragment as part of their outer coat on either the minor (pIII) or major (pVIII) coat protein. (wikipedia.org)
  • Antibodies
  • This technology was further developed and improved by groups at the Laboratory of Molecular Biology with Greg Winter and John McCafferty, The Scripps Research Institute with Lerner and Barbas and the German Cancer Research Center with Breitling and Dübel for display of proteins such as antibodies for therapeutic protein engineering. (wikipedia.org)
  • novel
  • Our new NEBNext® Ultra™ II FS DNA Library Prep Kit with novel fragmentation reagent meets the dual challenge of generating high quality next gen sequencing libraries from ever-decreasing input amounts AND simple scalability. (neb.com)
  • receptors
  • Clathrin coated vesicles enable neurotransmitter receptors and other proteins to be endocytosed or taken up across neuronal membranes and across the membranes of other types of cells. (wikipedia.org)
  • This enables a turnover of neuroreceptors or other proteins to be maintained and thus the numbers of receptors can be fine tuned. (wikipedia.org)
  • Biological
  • We need to better understand the biological mechanisms that lead to the development of breast and ovarian cancer before we attempt to attack it through targeted therapies aimed at causing DNA damage . (medicalxpress.com)
  • To meet such complicated demands in biological process via spatial and temporal proteolysis, protein substrates have to be recognized, recruited, and eventually hydrolyzed in a well controlled fashion. (wikipedia.org)
  • apoptosis
  • The mathematical relations that we have formulated can quantitatively determine how ablation of an oncogene's protein activity can result in apoptosis and/or a decrease in proliferation within a population of tumor cells. (biomedcentral.com)
  • It breaks up the DNA during apoptosis and promotes cell differentiation. (wikipedia.org)
  • DFFA is the substrate for caspase-3 and triggers DNA fragmentation during apoptosis. (wikipedia.org)
  • DFFB has been found to trigger both DNA fragmentation and chromatin condensation during apoptosis. (wikipedia.org)
  • Caspase 3 is responsible for cellular differentiation, although it is unclear how this kind of protein can promote the cell apoptosis. (wikipedia.org)
  • In the cytoplasm, the encoded protein may function to regulate apoptosis. (wikipedia.org)
  • regulate
  • Studies of the similar gene in mouse suggested that this protein may interact with, and regulate the activity of numerous protein kinases of the JNK signaling pathway, and thus function as a scaffold protein in neuronal cells. (wikipedia.org)
  • A few other mechanisms in E. coli that variously regulate initiation are DDAH (datA-Dependent DnaA Hydrolysis, which is also regulated by IHF), inhibition of the dnaA gene (by the SeqA protein), and reactivation of DnaA by the lipid membrane. (wikipedia.org)
  • kinase
  • The protein encoded by this gene is a tyrosine-protein kinase whose activity can be inhibited by phosphorylation by CSK. (wikipedia.org)
  • This induces long-range allostery via protein domain dynamics, causing the structure to be destabilized, resulting in the opening up of the SH3, SH2 and kinase domains and the autophosphorylation of the residue tyrosine 416. (wikipedia.org)
  • C-jun-amino-terminal kinase-interacting protein 3 is an enzyme that in humans is encoded by the MAPK8IP3 gene. (wikipedia.org)
  • After Fas stimulation, Daxx is activated and plays its role of pro-apoptotic protein in activating the c-JUN-N-Terminal Kinase (JNK) pathway. (wikipedia.org)
  • phosphorylation
  • Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular parts of a cell, or mark them for phosphorylation. (wikipedia.org)
  • The subcellular localization and function of this protein are modulated by post-translational modifications, including sumoylation, phosphorylation and polyubiquitination. (wikipedia.org)
  • interaction
  • Rieper, Anders and Vedral modelled the electron clouds of nucleic acids in a single strand of DNA as a chain of coupled quantum harmonic oscillators with dipole-dipole interaction between nearest neighbours. (xonl.de)
  • Applications of phage display technology include determination of interaction partners of a protein (which would be used as the immobilised phage "bait" with a DNA library consisting of all coding sequences of a cell, tissue or organism) so that the function or the mechanism of the function of that protein may be determined. (wikipedia.org)
  • The protein encoded by this gene shares similarity with the product of Drosophila syd gene, required for the functional interaction of kinesin I with axonal cargo. (wikipedia.org)
  • Several additional interacting proteins are known, but not always is there an understanding of the specific function and relevance of this interaction. (wikipedia.org)
  • According to the protein interaction and topological characteristics of this multisubunit complex, the 19S regulatory particle is composed of a base and a lid subcomplex. (wikipedia.org)
  • strand
  • The researchers hope to continue studying the role of BRCA1 in DNA double-strand break repair in order to determine whether the mutations they examined are important for the onset of cancer and whether targeted therapies can be developed. (medicalxpress.com)
  • CAD leads to the initiation of the DNA strand breakage, which occurs during terminal differentiation of some cell, such as skeletal muscle cell. (wikipedia.org)
  • It is hypothesized that DNA stretching by DnaA bound to the origin promotes strand separation which allows more DnaA to bind to the unwound region. (wikipedia.org)
  • H. salinarum is polyploid and highly resistant to ionizing radiation and desiccation, conditions that induce DNA double-strand breaks. (wikipedia.org)
  • metabolism
  • The three main purposes of metabolism are the conversion of food/fuel to energy to run cellular processes, the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates, and the elimination of nitrogenous wastes. (wikipedia.org)
  • Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter for example, the breaking down of glucose to pyruvate, by cellular respiration, and anabolism, the building up of components of cells such as proteins and nucleic acids. (wikipedia.org)
  • interact
  • NFIX has been shown to interact with SKI protein and it is also known to interact with AP-1. (wikipedia.org)
  • When Src is inactive, the phosphorylated tyrosine group at the 527 position interacts with the SH2 domain which helps the SH3 domain interact with the flexible linker domain and thereby keeps the inactive unit tightly bound. (wikipedia.org)
  • Furthermore
  • Furthermore, DNA polymerase III must be able to distinguish between correctly paired bases and incorrectly paired bases. (wikipedia.org)
  • helicase
  • Contains 1 helicase ATP-binding domain. (abcam.cn)
  • The DnaC helicase loader then interacts with the DnaA bound to the single-stranded DNA to recruit the DnaB helicase, which will continue to unwind the DNA as the DnaG primase lays down an RNA primer and DNA Polymerase III holoenzyme begins elongation. (wikipedia.org)
  • Domains
  • Src contains at least three flexible protein domains, which, in conjunction with myristoylation, can mediate attachment to membranes and determine subcellular localization. (wikipedia.org)
  • dsDNA
  • In addition, dsDNA (double stranded DNA) in the active site has a wider major groove and shallower minor groove that permits the formation of hydrogen bonds with the third nitrogen of purine bases and the second oxygen of pyrimidine bases. (wikipedia.org)
  • reagent
  • Cell routine evaluation After removal of methanol, cells had been treated having a Coulter DNA-Prep reagent package (Beckman-Coulter, France). (cancercurehere.com)
  • terminal
  • Recently published in the journal Aging, the study led by Kristoffer Valerie, Ph.D., discovered that certain BRCA1 mutations affecting the BRCA1 C-terminal (BRCT) binding site resulted in excessive DNA repair, or hyper-recombination, which may contribute to the development of breast and ovarian cancers. (medicalxpress.com)
  • The CLINT1 protein binds to the terminal domain of the clathrin heavy chain and stimulates clathrin cage vesicle assembly. (wikipedia.org)
  • conformation
  • Upon absorption of a photon, retinal changes conformation, causing a conformational change in the bacterioopsin protein which drives proton transport. (wikipedia.org)
  • mutations
  • Now, researchers at Virginia Commonwealth University Massey Cancer Center have shown that certain BRCA1 mutations result in excessive, uncontrolled DNA repair, which challenges the prior assumption that mutations in BRCA1 only contribute to breast cancer through a reduction in function. (medicalxpress.com)
  • fragmentation
  • Do you need a faster, more reliable solution for DNA fragmentation and library construction? (neb.com)
  • Caspase-activated DNase (CAD) or DNA fragmentation factor subunit beta is a protein that in humans is encoded by the DFFB gene. (wikipedia.org)
  • It is also known as caspase activated nuclease (CPAN), dna fragmentation factor 40 (DFF-40), DFF2 and DFFB. (wikipedia.org)
  • It remains inactive in growing cells while it is associated with its inhibitor (ICAD, DNA fragmentation factor 45 kDa subunit, DFFA or DFF45) resulting into a complex ICAD-CAD. (wikipedia.org)
  • Therefore, a cavity (active site) where DNA can fit is produced, even though there is another binding region responsible for stable DNA complex during its fragmentation. (wikipedia.org)
  • Per usual in non-apoptotic growing cells caspase activated dnase is held in check inactivated in the cytoplasm thanks to the association with its inhibitor, inhibitor of caspase-activated DNase (ICAD) also known as DNA fragmentation factor 45 kDa (DFF45). (wikipedia.org)
  • Functions
  • Functions in the recombinational DNA repair (RAD52) pathway. (abcam.cn)
  • In the nucleus, the encoded protein functions as a potent transcription repressor that binds to sumoylated transcription factors. (wikipedia.org)
  • Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape. (wikipedia.org)
  • domain
  • NFIX protein, human at the US National Library of Medicine Medical Subject Headings (MeSH) This article incorporates text from the United States National Library of Medicine, which is in the public domain. (wikipedia.org)
  • cell
  • SciBrow - SciBrow provides an interactive webbrowser environment for the visualisation of single cell genomics with the purpose of detecting contamination of given DNA contig scaffolds. (uni-bielefeld.de)
  • Targeting of p21 promoter is responsible for inducing cell differentiation, which is promoted by modifying the DNA nuclear microenvironment. (wikipedia.org)
  • In other words, it is possible that in fast growth conditions the grandmother cells starts replicating its DNA for grand daughter cell. (wikipedia.org)
  • They bind to DnaA-ADP and DnaA-ATP with equal affinities and are bound by DnaA throughout most of the cell cycle and forms a scaffold on which rest of the orisome assembles. (wikipedia.org)
  • The S-layer is made of a cell-surface glycoprotein, which accounts for approximately 50% of the cell surface proteins. (wikipedia.org)
  • The primary role of bacterioruberin in the cell is to protect against DNA damage incurred by UV light. (wikipedia.org)