Recognition of hyperacetylated N-terminus of H2AZ by TbBDF2 from Trypanosoma brucei

2017 ◽  
Vol 474 (22) ◽  
pp. 3817-3830 ◽  
Author(s):  
Xiao Yang ◽  
Xuelei Wu ◽  
Jiahai Zhang ◽  
Xuecheng Zhang ◽  
Chao Xu ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Binding Sites ◽  
Gene Expression Regulation ◽  
Binding Pocket ◽  
Lysine Acetylation ◽  
Biological Processes ◽  
Left Handed ◽  
N Terminus ◽  
Small Molecule Compound ◽  
Loop Regions

Histone modification plays an important role in various biological processes, including gene expression regulation. Bromodomain, as one of histone readers, recognizes specifically the ε-N-lysine acetylation (KAc) of histone. Although the bromodomains and histone acetylation sites of Trypanosoma brucei (T. brucei), a lethal parasite responsible for sleeping sickness in human and nagana in cattle, have been identified, how acetylated histones are recognized by bromodomains is still unknown. Here, the bromodomain factor 2 (TbBDF2) from T. brucei was identified to be located in the nucleolus and bind to the hyperacetylated N-terminus of H2AZ which dimerizes with H2BV. The bromodomain of TbBDF2 (TbBDF2-BD) displays a conserved fold that comprises a left-handed bundle of four α-helices (αZ, αA, αB, αC), linked by loop regions of variable length (ZA and BC loops), which form the KAc-binding pocket. NMR chemical shift perturbation further revealed that TbBDF2-BD binds to the hyperacetylated N-terminus of H2AZ through its KAc-binding pocket. By structure-based virtual screening combining with the ITC experiment, a small molecule compound, GSK2801, was shown to have high affinity to TbBDF2-BD. GSK2801 and the hyperacetylated N-terminus of H2AZ have similar binding sites on TbBDF2-BD. In addition, GSK2801 competitively inhibits the hyperacetylated N-terminus of H2AZ binding to TbBDF2-BD. After treatment of GSK2801, cell growth was inhibited and localization of TbBDF2 was disrupted. Our results report a novel bromodomain-histone recognition by TbBDF2-BD and imply that TbBDF2 may serve as a potential chemotherapeutic target for the treatment of trypanosomiasis.

scholarly journals SiteOut: an online tool to design binding site-free DNA sequences

2015 ◽  
Author(s):  
Javier Estrada ◽  
Teresa Ruiz-Herrero ◽  
Clarissa Scholes ◽  
Zeba Wunderlich ◽  
Angela DePace
Keyword(s):  
Binding Site ◽  
Dna Sequences ◽  
Binding Sites ◽  
Regulatory Proteins ◽  
Biological Processes ◽  
Major Goal ◽  
Specific Sequence ◽  
Online Tool ◽  
Protein Binding Sites ◽  
Regulatory Dna

DNA-binding proteins control many fundamental biological processes such as transcription, recombination and replication. A major goal is to decipher the role that DNA sequence plays in orchestrating the binding and activity of such regulatory proteins. To address this goal, it is useful to rationally design DNA sequences with desired numbers, affinities and arrangements of protein binding sites. However, removing binding sites from DNA is computationally non-trivial since one risks creating new sites in the process of deleting or moving others. Here we present an online binding site removal tool, SiteOut, that enables users to design arbitrary DNA sequences that entirely lack binding sites for factors of interest. SiteOut can also be used to delete sites from a specific sequence, or to introduce site-free spacers between functional sequences without creating new sites at the junctions. In combination with commercial DNA synthesis services, SiteOut provides a powerful and flexible platform for synthetic projects that interrogate regulatory DNA. Here we describe the algorithm and illustrate the ways in which SiteOut can be used; it is publicly available at https://depace.med.harvard.edu/siteout/

scholarly journals Circular RNA circ_0014717 Suppresses Hepatocellular Carcinoma Tumorigenesis Through Regulating miR-668-3p/BTG2 Axis

2021 ◽  
Vol 10 ◽  
Author(s):  
Hongxi Ma ◽  
Chunchun Huang ◽  
Qiuhuan Huang ◽  
Guangzhi Li ◽  
Jun Li ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Binding Sites ◽  
Close Association ◽  
Circular Rna ◽  
Migration And Invasion ◽  
Biological Processes ◽  
Tissue Samples ◽  
Qrt Pcr ◽  
Direct Binding ◽  
Hep3b Cells

Recent studies have reported a close association between circRNAs and cancer development. CircRNAs have been recognized to be involved in various biological processes. Up to now, the function of circRNAs in hepatocellular carcinoma (HCC) is still poorly known. qRT-PCR was used to test circ_0014717 expression in HCC tissue samples and cells was determined. It was shown that circ_0014717 was significantly decreased in HCC. Then, we observed overexpression of circ_0014717 obviously repressed HCC cell growth, migration and invasion. Next, we predicted circ_0014717 acted as a sponge of miR-668-3p. miR-668-3p has been reported to participate in several diseases. In our work, it was shown miR-668-3p was greatly increased in HCC and the direct binding sites between circ_0014717 and miR-668-3p were validated. In addition, B-cell translocation gene 2 (BTG2) is closely involved in cellular carcinogenic processes. BTG2 was predicted as a target for miR-668-3p. By performing rescue assays, we demonstrated that circ_0014717 repressed HCC progression via inhibiting BTG2 expression and sponging miR-668-3p. It was manifested loss of circ_0014717 induced HCC progression, which was reversed by BTG2 in Hep3B cells. In conclusion, our findings illustrated a novel circ_0014717/miR-668-3p/BTG2 regulatory signaling pathway in HCC.

scholarly journals The phosphoprotein (P) and L binding sites reside in the N-terminus of the L subunit of the measles virus RNA polymerase

Virology ◽  
2004 ◽  
Vol 327 (2) ◽  
pp. 297-306 ◽  
Author(s):  
Bayram Cevik ◽  
David E. Holmes ◽  
Emmanuel Vrotsos ◽  
Joyce A. Feller ◽  
Sherin Smallwood ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Binding Sites ◽  
Measles Virus ◽  
Virus Rna ◽  
N Terminus

Abstract MP20: Optogenetic Control Of Pip2 To Assess Mechanisms Regulating The Epithelial Sodium Channel

Hypertension ◽  
2021 ◽  
Vol 78 (Suppl_1) ◽  
Author(s):  
Crystal R Archer ◽  
Amanpreet Kaur ◽  
Tarek Mohamed ◽  
James D Stockand
Keyword(s):  
Binding Sites ◽  
Hek293 Cells ◽  
Proper Function ◽  
Small Decrease ◽  
Kidney Tubules ◽  
Wild Type ◽  
N Terminus ◽  
Patch Clamp Electrophysiology ◽  
G Protein Coupled

The epithelial Na + channel (ENaC) plays a key role in Na + transport in epithelial linings to include the lung, colon and kidney. In the distal kidney tubules, ENaC regulates Na + reabsorption and blood volume. Thus, dysfunctions in signaling pathways regulating ENaC activity are linked to hypertension or hypotension. Phosphatidylinositol 4,5-bisphosphate (PIP 2 ) is a target of the G protein coupled receptor P2Y2 pathway, and is necessary for the proper function of ENaC. This nonvoltage-gated trimeric channel is comprised of α, β, and γ subunits. We recently described two intracellular PIP 2 binding sites on the N termini of β-, and γ-ENaC, with moderate μM affinity. Here, we report the functional effects on ENaC containing a combination of mutations to those PIP 2 binding sites, by controlled depletion of PIP 2 . We used a CIBN/CRY2-5-ptase optogenetic dimerization system to deplete PIP 2 levels in HEK293 cells transiently expressing wild type (wt) ENaC or the mutant ENaC constructs. A fluorescent Na + indicator, was used to monitor ENaC activity by tracking the relative intracellular Na + levels. Upon optogenetic-controlled depletion of PIP 2 , Na + levels decreased in cells expressing wt ENaC. Mutations to the PIP 2 sites of ENaC were expected to have no change in Na + levels upon PIP 2 depletion due to the disruption of PIP 2 binding. As a control, mutations to non-PIP 2 binding sites were included, and were expected to have decreased Na + levels similar to wt ENaC. Interestingly, mutation of each independent PIP 2 site resulted in only a small decrease of intracellular Na + , compared to wt ENaC. However, mutations throughout the entire N-terminus of β-ENaC, including the PIP 2 binding site, resulted in a significant increase of Na + upon PIP 2 depletion. We performed patch clamp electrophysiology and found that the ENaC recordings corresponded to the Na + fluctuations. These data suggest that the residues surrounding the PIP 2 binding sites play a significant role in the affinity of PIP 2 for ENaC. The role of these other domains in PIP 2 binding is still under investigation.

GEREDB: Gene expression regulation database curated by mining abstracts from literature

2019 ◽  
Vol 17 (04) ◽  
pp. 1950024 ◽  
Author(s):  
Tinghua Huang ◽  
Xiali Huang ◽  
Bomei Shi ◽  
Min Yao
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Gene Expression Regulation ◽  
Biological Database ◽  
Biological Processes ◽  
Expression Data ◽  
Biological Responses ◽  
Human Genes ◽  
The Relationship ◽  
Made In

Understanding how genes are expressed and regulated in different biological processes are fundamental and challenging issues. Considerable progress has been made in studying the relationship between the expression and regulation of human genes. However, it is difficult to use these resources productively to analyze gene expression data. GEREDB ( www.thua45.cn/geredb ) has been developed to facilitate analyses that will provide insights into the regulation of genes that govern specific biological responses. GEREDB is a publicly available, manually curated biological database that stores the data regarding relationships between expression and regulation of human genes. To date, more than 39,000 Links have been contextually annotated by reviewing more than 53,000 abstracts. GEREDB can be searched using the official NCBI gene symbol as a query, and it can be downloaded along with the GEREA software package. GEREDB has the ability to analyze user-supplied gene expression data in a causal analysis oriented manner using the GEREA bioinformatics tool.

scholarly journals Etomidate and Etomidate Analog Binding and Positive Modulation of γ-Aminobutyric Acid Type A Receptors

2018 ◽  
Vol 129 (5) ◽  
pp. 959-969 ◽  
Author(s):  
Megan McGrath ◽  
Zhiyi Yu ◽  
Selwyn S. Jayakar ◽  
Celena Ma ◽  
Mansi Tolia ◽  
...  
Keyword(s):  
Steric Hindrance ◽  
Gabaa Receptors ◽  
Binding Sites ◽  
Phenyl Ring ◽  
Type A ◽  
Binding Pocket ◽  
Aminobutyric Acid ◽  
Substituent Group ◽  
Acid Type ◽  
Site Selective

Abstract Editor’s Perspective What We Already Know about This Topic What This Article Tells Us That Is New Background Naphthalene-etomidate, an etomidate analog containing a bulky phenyl ring substituent group, possesses very low γ-aminobutyric acid type A (GABAA) receptor efficacy and acts as an anesthetic-selective competitive antagonist. Using etomidate analogs containing phenyl ring substituents groups that range in volume, we tested the hypothesis that this unusual pharmacology is caused by steric hindrance that reduces binding to the receptor’s open state. Methods The positive modulatory potencies and efficacies of etomidate and phenyl ring–substituted etomidate analogs were electrophysiology defined in oocyte-expressed α1β3γ2L GABAA receptors. Their binding affinities to the GABAA receptor’s two classes of transmembrane anesthetic binding sites were assessed from their abilities to inhibit receptor labeling by the site-selective photolabels 3[H]azi-etomidate and tritiated R-5-allyl-1-methyl-5-(m-trifluoromethyl-diazirynylphenyl) barbituric acid. Results The positive modulatory activities of etomidate and phenyl ring–substituted etomidate analogs progressively decreased with substituent group volume, reflecting significant decreases in both potency (P = 0.005) and efficacy (P < 0.0001). Affinity for the GABAA receptor’s two β+ − α– anesthetic binding sites similarly decreased with substituent group volume (P = 0.003), whereas affinity for the receptor’s α+ – β–/γ+ – β– sites did not (P = 0.804). Introduction of the N265M mutation, which is located at the β+ − α– binding sites and renders GABAA receptors etomidate-insensitive, completely abolished positive modulation by naphthalene-etomidate. Conclusions Steric hindrance selectively reduces phenyl ring–substituted etomidate analog binding affinity to the two β+ − α– anesthetic binding sites on the GABAA receptor’s open state, suggesting that the binding pocket where etomidate’s phenyl ring lies becomes smaller as the receptor isomerizes from closed to open.

scholarly journals PRIME-3D2D is a 3D2D model to predict binding sites of protein–RNA interaction

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Juan Xie ◽  
Jinfang Zheng ◽  
Xu Hong ◽  
Xiaoxue Tong ◽  
Shiyong Liu
Keyword(s):  
Full Advantage ◽  
High Throughput ◽  
Binding Sites ◽  
High Throughput Sequencing ◽  
Secondary Structures ◽  
Biological Processes ◽  
Genome Wide ◽  
Rna Interaction ◽  
Rna Complexes ◽  
Better Than

AbstractProtein-RNA interaction participates in many biological processes. So, studying protein–RNA interaction can help us to understand the function of protein and RNA. Although the protein–RNA 3D3D model, like PRIME, was useful in building 3D structural complexes, it can’t be used genome-wide, due to lacking RNA 3D structures. To take full advantage of RNA secondary structures revealed from high-throughput sequencing, we present PRIME-3D2D to predict binding sites of protein–RNA interaction. PRIME-3D2D is almost as good as PRIME at modeling protein–RNA complexes. PRIME-3D2D can be used to predict binding sites on PDB data (MCC = 0.75/0.70 for binding sites in protein/RNA) and transcription-wide (MCC = 0.285 for binding sites in RNA). Testing on PDB and yeast transcription-wide data show that PRIME-3D2D performs better than other binding sites predictor. So, PRIME-3D2D can be used to predict the binding sites both on PDB and genome-wide, and it’s freely available.

scholarly journals Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy

2020 ◽  
Vol 21 (8) ◽  
pp. 2673 ◽  
Author(s):  
Kwang-Im Oh ◽  
Jinwoo Kim ◽  
Chin-Ju Park ◽  
Joon-Hwa Lee
Keyword(s):  
Nmr Spectroscopy ◽  
Biological Function ◽  
Conformational Exchange ◽  
Biological Processes ◽  
Dynamic Characterization ◽  
Dynamic Features ◽  
Dna Structures ◽  
Left Handed ◽  
G Quadruplex ◽  
Insight Into

The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.

scholarly journals The Retinoid and Non-Retinoid Ligands of the Rod Visual G Protein-Coupled Receptor

2019 ◽  
Vol 20 (24) ◽  
pp. 6218 ◽  
Author(s):  
Joseph T. Ortega ◽  
Beata Jastrzebska
Keyword(s):  
Drug Discovery ◽  
G Protein ◽  
Binding Sites ◽  
Binding Pocket ◽  
Biologically Active ◽  
Surface Receptors ◽  
Beneficial Effects ◽  
Light Sensing ◽  
Potential Binding ◽  
G Protein Coupled

G protein-coupled receptors (GPCRs) play a predominant role in the drug discovery effort. These cell surface receptors are activated by a variety of specific ligands that bind to the orthosteric binding pocket located in the extracellular part of the receptor. In addition, the potential binding sites located on the surface of the receptor enable their allosteric modulation with critical consequences for their function and pharmacology. For decades, drug discovery focused on targeting the GPCR orthosteric binding sites. However, finding that GPCRs can be modulated allosterically opened a new venue for developing novel pharmacological modulators with higher specificity. Alternatively, focus on discovering of non-retinoid small molecules beneficial in retinopathies associated with mutations in rhodopsin is currently a fast-growing pharmacological field. In this review, we summarize the accumulated knowledge on retinoid ligands and non-retinoid modulators of the light-sensing GPCR, rhodopsin and their potential in combating the specific vision-related pathologies. Also, recent findings reporting the potential of biologically active compounds derived from natural products as potent rod opsin modulators with beneficial effects against degenerative diseases related to this receptor are highlighted here.

Defining a second epitope for heparin-induced thrombocytopenia/thrombosis antibodies using KKO, a murine HIT-like monoclonal antibody

Blood ◽  
2002 ◽  
Vol 99 (4) ◽  
pp. 1230-1236 ◽  
Author(s):  
Zhong Q. Li ◽  
Weiyi Liu ◽  
Kwang S. Park ◽  
Brue S. Sachais ◽  
Gowthani M. Arepally ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Binding Site ◽  
Binding Sites ◽  
Heparin Therapy ◽  
Common Complication ◽  
Platelet Factor ◽  
Heparin Induced Thrombocytopenia ◽  
The Third ◽  
N Terminus ◽  
A Site

Heparin-induced thrombocytopenia/thrombosis (HIT/T) is a common complication of heparin therapy that is caused by antibodies to platelet factor 4 (PF4) complexed with heparin. The immune response is polyclonal and polyspecific, ie, more than one neoepitope on PF4 is recognized by HIT/T antibodies. One such epitope has been previously identified; it involves the domain between the third and fourth cysteine residues in PF4 (site 1). However, the binding sites for other HIT/T antibodies remain to be defined. To explore this issue, the binding site of KKO, an HIT/T-like murine monoclonal antibody, was defined. KKO shares a binding site with many HIT/T antibodies on PF4/heparin, but does not bind to site 1 or recognize mouse PF4/heparin. Therefore, the binding of KKO to a series of mouse/human PF4 chimeras complexed with heparin was examined. KKO recognizes a site that requires both the N terminus of PF4 and Pro34, which immediately precedes the third cysteine. Both regions lie on the surface of the PF4 tetramer in sufficient proximity (within 0.74 nm) to form a contiguous antigenic determinant. The 10 of 14 HIT/T sera that require the N terminus of PF4 for antigen recognition also require Pro34 to bind. This epitope, termed site 2, lies adjacent to site 1 in the crystal structure of the PF4 tetramer. Yet sites 1 and 2 can be recognized by distinct populations of antibodies. These studies further help to define a portion of the PF4 tetramer to which self-reactive antibodies develop in patients exposed to heparin.

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