• The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. (nih.gov)
  • The process of canonical autophagy follows a hierarchical-ordered recruitment of autophagy-related (ATG) proteins to the phagophore assembly site [ 5 ]. (hindawi.com)
  • Interestingly, recent data suggest a function for ULK1 not only during autophagy activation but also during elongation and closure of the autophagosomal membrane via binding to ATG8 proteins [ 8 ]. (hindawi.com)
  • Pentatricopeptide repeat (PPR) proteins are sequence-specific RNA-binding proteins that form a pervasive family of proteins conserved in yeast, plants, and humans. (rcsb.org)
  • this family of proteins is hereafter called EBF) are a group of DNA-binding transcription factors with the basic helix-loop-helix (bHLH) domain. (aacrjournals.org)
  • DNA meth-ylation represses transcription by interfering with transcription factor binding and indirectly by recruiting methyl-CpG-binding proteins and reducing chromatin remodeling activities ( 12 ). (spandidos-publications.com)
  • its binding is stimulated by other ribosomal proteins, e.g. (proteopedia.org)
  • HAMAP-Rule:MF_01331_B] [ RL4_DEIRA ] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. (proteopedia.org)
  • We found that antibiotic binding sites are composed exclusively of segments of 23S ribosomal RNA at the peptidyl transferase cavity and do not involve any interaction of the drugs with ribosomal proteins. (proteopedia.org)
  • DNA virus encoded proteins interact with host cellular signaling pathways and control proliferation, cell death and genomic integrity viral oncoproteins are known to bind cellular Deubiquitinates (DUBs) such as cyclindromatosis tumor suppressor, ubiquitin-specific proteases 7, 11, 15 and 20, and A-20 to improve their intracellular stability and cellular signaling pathways and finally transformation. (bvsalud.org)
  • Transcriptional regulation information for a gene, including any predicted DNA binding site motifs ( YeTFaSCo ) for the gene's protein product, as well as any of its targets (genes it regulates) or regulators (genes that regulate it), based on experimental evidence. (yeastgenome.org)
  • This table lists putative transcriptional regulatory targets for the central gene represented on this page. (yeastgenome.org)
  • Primer extension analysis identified a transcriptional start site 72 bp upstream of the pckA initiation codon and an upstream sequence similar to ς 70 promoters. (asm.org)
  • Therefore, EBF3 regulates a transcriptional program underlying a putative tumor suppression pathway. (aacrjournals.org)
  • The present study investigated the methylation of CpG sites in the cyclooxygenase (COX)‑2 promoter via nuclear factor (NF)‑κB transcriptional regulation and elucidated its effect on the COX‑2 transcriptional expression in a ketamine‑induced ulcerative cystitis (KIC) animal model. (spandidos-publications.com)
  • Amino acid substitution sites, key amino acids for virulence and receptor binding in BCoV, and cleavage sites are shown. (cdc.gov)
  • Amino acids of putative cleavage sites are underlined. (cdc.gov)
  • 3028 /gene="ORF1" /locus_tag="NoVGII_gp1" /product="VPg" /note="For Southampton calicivirus, both N-terminal and C-terminal cleavage sites have been confirmed by direct sequencing. (cdc.gov)
  • We hypothesized that a comprehensive analysis of genetic variations found within the 3' untranslated region of genes predicted to affect miRNA binding (miRSNP) can identify additional prostate cancer risk variants. (ox.ac.uk)
  • We mapped all estrogen receptor and RNA polymerase II binding sites on a genome-wide scale, identifying the authentic cis binding sites and target genes, in breast cancer cells. (nature.com)
  • Studies on rodent UGT genes have demonstrated that the transcription factors hepatocyte nuclear factor 1 (HNF1) and CAAT-enhancer binding protein are important positive regulators of UGT expression in the liver (Hansen et al. (aspetjournals.org)
  • In a genome-wide screen for putative tumor suppressor genes, the EBF3 locus on the human chromosome 10q26.3 was found to be deleted or methylated in 73% of the examined cases of brain tumors. (aacrjournals.org)
  • In particular, mutations in DNA binding sites recognized by transcription factors can alter regulator binding affinities and, consequently, expression of target genes. (biomedcentral.com)
  • Therefore, the purpose of the present study was to investigate the genetic alteration as well as assess their effects on the receptor binding domain (RBD) of the spike and the putative RNA binding site of the RdRp genes of SARS-CoV-2 using bioinformatics tools. (bvsalud.org)
  • The primase pUL70 contains several conserved motifs or regions, including a region (residues 881-920) that corresponds to a putative zinc-finger pattern shown to play essential role in HSV-1 ( Biswas and Weller, 1999 ). (frontiersin.org)
  • The 4 critical sugar-binding residues are indicated by black dots. (cdc.gov)
  • Structural analysis revealed that THA8L contains two extensive patches of positively charged residues next to the residues that are proposed to comprise the RNA-binding codes. (rcsb.org)
  • On the basis of these data, we constructed a model of THA8L-RNA binding that is dependent on two forces: one is the interaction between nucleotide bases and specific amino acids in the PPR motifs (codes), and the other is the interaction between the negatively charged RNA backbone and positively charged residues of PPR motifs. (rcsb.org)
  • Figure 4: Identification of enriched motifs within the estrogen receptor binding sites and validation of transcription factor binding. (nature.com)
  • Binding sites motifs as predicted by YeTFaSCo . (yeastgenome.org)
  • Here we present analysis of transcription factor binding motifs co-localized with non-coding variants. (biomedcentral.com)
  • Such stability of binding motifs is even more exhibited in DNase accessible regions. (biomedcentral.com)
  • Further analysis of transcription factors with conserved binding motifs can reveal cell regulatory pathways crucial for the survivability of various human cancers. (biomedcentral.com)
  • These targets were identified based on the presence of predicted regulator binding sites or experimental regulator binding in the target promoter, and/or changes in the target gene's transcript levels in regulator mutant strains. (yeastgenome.org)
  • In silico analysis identified putative nuclear factor of activated T cell (NFAT) binding sites in the CSE promoter. (unboundmedicine.com)
  • EBF3 bound directly to p21 cip1/waf1 promoter and regulated transcription from both p21 cip1/waf1 and p27 kip1 promoters in reporter assays. (aacrjournals.org)
  • Ketamine treatment increased the binding of NF‑κB and permissive histone H3 lysine‑4 (H3K4)m3, but caused a decrease in the repressive histone H3K27m3 and H3K36m3 on the COX‑2 promoter ranging from ‑1,522 to ‑1,331 bp as determined by a chromatin immunoprecipitation assay. (spandidos-publications.com)
  • The mechanism of epigenetic regulation involves the CpG site methylation of promoter regions and the modification of DNA and histones by altering chromatin structure ( 9 - 11 ). (spandidos-publications.com)
  • By using sequence alignment of herpesviruses homologs, we identified conserved amino acids in the putative pUL105 ATP binding site and in the putative pUL70 zinc finger pattern. (frontiersin.org)
  • For this purpose, NLRP3 homology model was built and the putative protein binding region of a non-covalent inhibitor MCC950 (used as a probe) was investigated using a combination of in silico techniques. (mdpi.com)
  • Newman, Kahlan E. and Khalid, Syma (2023) Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. (soton.ac.uk)
  • These conserved families of secreted morphogens/signals, such as Fibroblast Growth Factor (FGF), Hedgehog (Hh), Wingless (Wg)/Wnt, Epidermal Growth Factor (EGF), and Decapentaplegic (Dpp - a BMP homolog), act away from their sources and, upon binding to receptors, activate gene regulatory pathways to induce functions in recipient cells 1 , 2 . (biorxiv.org)
  • The crystal structures of the 17β-HSDcl apo, holo and coumestrol-inhibited ternary complex, and the active-site Y167F mutant reveal subtle conformational differences in the substrate-binding loop that probably modulate the catalytic activity of 17β-HSDcl. (rcsb.org)
  • at 100 μM substrate (4-oestrene-3,17-dione)] by occupying the putative steroid-binding site. (rcsb.org)
  • The main aim was to detect putative protein hot spots involved in the stabilization of protein-ligand complex. (mdpi.com)
  • In one study of a large set of protein-ligand complexes, we tried to improve the free energies of binding by using MD simulations with QM-derived charges, which sometimes led to improved results, but not always. (lu.se)
  • Additionally, we compared how MD and grand-canonical Monte Carlo (GCMC) can be used to assess dynamics and thermodynamics of protein-ligand binding for both buried and solvent-exposed binding sites. (lu.se)
  • There are also 4 nuclear localization signals and 7 O-linked glycosylation sites. (wikipedia.org)
  • Thus far, SELEX experiments have been very good at suggesting the highest affinity oligonucleotide, but modeling lower affinity recognition site variants has been difficult. (projecteuclid.org)
  • For many transcription factors, including multiple members of FOX, HOX, and NR families, we show that human cancers accumulate fewer mutations than expected by chance that increase or decrease affinity of predicted binding sites. (biomedcentral.com)
  • Assessment of potential binding affinity changes induced by substitutions allows studying selection of sequence variants in binding sites in a way resembling usage of non-synonymous and synonymous substitutions in codons. (biomedcentral.com)
  • The molecular docking analysis revealed that the T478K mutation in RBD had the highest binding affinity. (bvsalud.org)
  • Conclusion: Our results indicated that double mutations (T478K and N501Y) in the S protein might increase the binding affinity of SARS-CoV-2 to human ACE2 compared to the wild-type (WT) strain. (bvsalud.org)
  • Mutations in these two positively charged patches greatly reduced THA8L RNA-binding activity. (rcsb.org)
  • The results showed that four of six mutations (L452R, T478K, N501Y, and D614G) in RBD and three of eight in the putative RNA binding site (P314L, E1084D, V1883T) were missense. (bvsalud.org)
  • Figure 3: Estrogen receptor and RNA PolII binding relative to specific gene targets. (nature.com)
  • In drug discovery, it is of utmost importance to accurately calculate the free energies of binding ligands to various protein targets, such as enzymes and receptors. (lu.se)
  • Figure 1: Summary of estrogen receptor and RNA PolII binding sites and correlation with nucleotide and gene number. (nature.com)
  • The class 1A phosphoinositide 3-kinase (PI3K) beta (PI3Kβ) is functionally unique in the ability to integrate signals derived from receptor tyrosine kinases (RTKs), heterotrimeric guanine nucleotide-binding protein (G-protein)-coupled receptors (GPCRs), and Rho-family GTPases. (elifesciences.org)
  • Figure 2: Estrogen-mediated transcript changes and correlation with estrogen receptor binding. (nature.com)
  • Figure 7: Assessment of estrogen receptor binding properties in different cell systems. (nature.com)
  • In the version of this article initially published online, the estrogen receptor and RNA PolII binding data were aligned incorrectly in the top panel of Figure 3, which represents estrogen receptor binding at the ESR1 gene region. (nature.com)
  • Amino acid sites shown to affect S1-mediated receptor binding in BCoV are highlighted in dark gray. (cdc.gov)
  • TGF-β signaling is initiated when the ligand binds to type II serine/threonine kinase receptor (TGFBR2), which then phosphorylates and activates type I serine/threonine kinase receptor (TGFBR1) [ 13 ]. (degruyter.com)
  • This inhibition has been attributed to the phosphorylation of the serine hydroxyl group in the active site of AChE. (cdc.gov)
  • Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. (lu.se)
  • the c-terminal membrane-binding portion contributes to the Golgi disassembly and, therefore, functionally similar to the picornavirus 2B protein" /protein_id="YP_009238492.1" mat_peptide 995. (cdc.gov)
  • The TTC16 gene is located on human chromosome 9 at site 9q34.11. (wikipedia.org)
  • We identified several putative THA8L-binding sites, enriched with purine sequences, in the group II introns. (rcsb.org)
  • Comparison of chlorpyrifos-oxon and paraoxon acetylcholinesterase inhibition dynamics: potential role of a peripheral binding site. (cdc.gov)
  • A Large-Scale Analysis of Genetic Variants within Putative miRNA Binding Sites in Prostate Cancer. (ox.ac.uk)
  • DNMT1 preserves the methyltransferase by binding to hemi-methylated CpG sites and methylates the cytosine on the newly synthesized strand after DNA replication, whereas DNMT3a/DNMT3b are required for the de novo genomic methylation of DNA ( 15 ). (spandidos-publications.com)
  • Diisocyanates bind select- diisocyanate exposure (Chiung et al. (cdc.gov)
  • Our SELEX model outperformed other published methods for predicting putative binding sites for Bicoid as indicated by the results of an in-vivo ChIP-chip experiment. (projecteuclid.org)
  • Subsequent un-anchoring of FGFR-bound-FGF from the source cell membrane dissociates cytoneme contacts and delivers FGF target-specifically to ASP cytonemes for paracrine functions. (biorxiv.org)
  • However, recent advances in microscopy revealed that both signal-producing and receiving cells could extend signaling filopodia named cytonemes and selectively deliver or receive signals through cytoneme-cell contact sites 4 - 9 . (biorxiv.org)
  • Typically, a predilection exists for distal limbs as the site of disease onset and more severe symptoms and signs. (medscape.com)
  • We propose that these steps result in the interconversion of DNA-binding sites in the catalytic core of condensin, forming the basis of the DNA translocation and loop-extrusion activities. (nature.com)
  • OmpB contains a potential Fe(III)-binding site and a fibronectin type III domain, suggesting a possible role for this protein in accessing Fe(III) oxides. (nih.gov)
  • Luciferase analysis was used to identify the binding site of miR-146a-3p and SIRT1. (medsci.org)
  • In addition to an extensive hydrogen-bonding network, coumestrol binding is stabilized further by π-π stacking interactions with Tyr212. (rcsb.org)
  • Here we report the details of antibiotic interactions with the components of their binding sites. (proteopedia.org)
  • To address this gap in our understanding of PI3Kβ regulation, we established an assay to directly visualize and decipher how three binding interactions regulate PI3Kβ when presented to the kinase in a biologically relevant configuration on supported lipid bilayers. (elifesciences.org)
  • metal site is extended X-ray absorption fine structure (EXAFS). (lu.se)
  • Furthermore, it is important and challenging to accurately model the large entropic contribution to ligand-binding free energies. (lu.se)
  • Our results also show the importance of putative Mg+2 ions for the binding of some drugs. (proteopedia.org)
  • This complex condition results in the flow of portal blood containing putative toxins produced in the gut to the systemic circulation and, ultimately, the brain via extrahepatic shunts (collateral flow). (medscape.com)
  • Our structures of the five-subunit condensin holo complex at different functional stages suggest that ATP binding induces the transition of the SMC coiled coils from a folded-rod conformation into a more open architecture. (nature.com)
  • The binding sites of miR-128-3p and TGFBR2 were predicted by Targetscan online software and confirmed by dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. (degruyter.com)
  • They have shown that metal sites in crystal structures are frequently photoreduced or disordered, which makes the interpretation of the structures hard. (lu.se)
  • Ribosomes, the site of protein synthesis, are a major target for natural and synthetic antibiotics. (proteopedia.org)
  • In addition, a reference to a website containing reference data files was omitted from the main text and Supplementary Note. (nature.com)
  • Moreover, the CpG site methylation is mediated by DNA methyltransferases (DNMTs), which catalyze the addition of a methyl group to cytosine ( 13 , 14 ). (spandidos-publications.com)
  • In addition, 35 RBD samples (89.7%) and 33 putative RNA binding site samples (84.6%) were similar to the Delta variant. (bvsalud.org)
  • Amino acid sites central to virulence in BCoV are highlighted in light gray. (cdc.gov)
  • Detailed knowledge of antibiotic binding sites is central to understanding the mechanisms of drug action. (proteopedia.org)
  • Our data demonstrate negative selection against binding sites alterations and suggest that such selection pressure protects cancer cells from rewiring of regulatory circuits. (biomedcentral.com)
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  • Find support for a specific problem in the support section of our website. (mdpi.com)
  • Wells were blocked with 1% BSA/Gelatin (KPL #50-61-00) for 1 hour at 37ºC to prevent non-specific binding, then the buffer was suctioned off and capture plates were stored at -80ºC with desiccant in plastic bags. (cdc.gov)