gebhart/patrepeval huggingface dataset:
The 5′ Binding MID Domain of Human Argonaute2 Tolerates Chemically Modified Nucleotide Analogues (2013)

Small interfering RNAs (siRNAs) can trigger potent gene silencing through the RNA interference (RNAi) pathway. The RNA-induced silencing complex (RISC) is key to this targeted mRNA degradation, and the human Argonaute2 (hAGO2) endonuclease component of RISC is responsible for the actual mRNA cleavage event. During RNAi, hAGO2 becomes loaded with the siRNA guide strand, making several key nucleic acid-enzyme interactions. Chemically modified siRNAs are now widely used in place of natural double-stranded RNAs, and understanding the effects chemical modifications have on guide strand-hAGO2 interactions has become particularly important. Here, interactions between the 5' nucleotide binding domain of hAGO2, MID, and chemically modified nucleotide analogues are investigated. Measured dissociation constants reveal that hAGO2 does not discriminate between nucleotide analogues during binding, regardless of the preferred sugar conformation of the nucleotide analogues. These results correlate well with cell-based gene silencing results employing siRNAs with 5'-modified guide strands. Additionally, chemical modification with 2'-deoxy-2'-fluoroarabino nucleic acid (2'F-ANA) and 2'-deoxy-2'-fluororibonucleic acid (2'F-RNA) at the passenger strand cleavage site of siRNAs has been shown to prevent hAGO2-mediated strand cleavage, an observation that appears to have little impact on overall gene silencing potency.
Platinum Group Organometallics Based on “Pincer” Complexes: Sensors, Switches, and Catalysts (2001)

Since the first reports in the late 1970s on transition metal complexes containing pincer-type ligands-named after the particular coordination mode of these ligands-these systems have attracted increasing interest owing to the unusual properties of the metal centers imparted by the pincer ligand. Typically, such a ligand comprises an anionic aryl ring which is ortho,ortho-disubstituted with heteroatom substituents, for example, CH<sub>2</sub> NR<sub>2</sub> , CH<sub>2</sub> PR<sub>2</sub> or CH<sub>2</sub> SR, which generally coordinate to the metal center, and therefore support the M-C σ bond. This commonly results in a terdentate and meridional coordination mode consisting of two metallacycles which share the M-C bond. Detailed studies of the formation and the properties of a large variety of pincers containing platinum group metal complexes have provided direct access to both a fundamental understanding of a variety of reactions in organometallic chemistry and to a range of new applications of these complexes. The discovery of alkane dehydrogenation catalysts, the mechanistic elucidation of fundamental transformations (for example, C-C bond activation), the construction of the first metallodendrimers for sustainable homogeneous catalysis, and the engineering of crystalline switches for materials processing represent only a few of the many highlights which have emanated from these numerous investigations. This review discusses the synthetic methodologies that are currently available for the preparation of platinum group metal complexes containing pincer ligands and especially emphasizes different applications that have been realized in materials science such as the development and engineering of sensors, switches, and catalysts.
A myocardin-related transcription factor regulates activity of serum response factor in Drosophila (2004)

Serum response factor (SRF) regulates genes involved in cell proliferation, migration, cytoskeletal organization, and myogenesis. Myocardin and myocardin-related transcription factors (MRTFs) act as powerful transcriptional coactivators of SRF in mammalian cells. We describe an MRTF from Drosophila, called DMRTF, which shares high homology with the functional domains of mammalian myocardin and MRTFs. DMRTF forms a ternary complex with and stimulates the activity of Drosophila SRF, which has been implicated in branching of the tracheal (respiratory) system and formation of wing interveins. A loss-of-function mutation introduced into the DMRTF locus by homologous recombination results in abnormalities in tracheal branching similar to those in embryos lacking SRF. Misexpression in wing imaginal discs of a dominant negative DMRTF mutant also causes a diminution of wing interveins, whereas overexpression of DMRTF results in excess intervein tissue, abnormalities reminiscent of SRF loss- and gain-of-function phenotypes, respectively. Overexpression of these DMRTF mutants in mesoderm and in the tracheal system also perturbs mesoderm cell migration and tracheal branching, respectively. We conclude that the interaction of MRTFs with SRF represents an ancient protein partnership involved in cytoplasmic outgrowth and cell migration during development.
Encapsulation of the cobra cytotoxin P4 in liposomes (1993)

Cytotoxin P4 isolated from the venom of the cobra Naja nigricollis nigricollis was encapsulated in liposomes by the reverse-phase evaporation method using phosphatidylcholine, cholesterol and phosphatidylethanolamine at molar ratios of 3:1:1. Cytotoxicity examination on murine melanoma B16F10 revealed that the activity of the entrapped cytotoxin did not change significantly and remained stable for at least 1 year at 4 degrees C without any significant leak from the liposomes (< 1%). Moreover, the activity of the cytotoxic liposomes was 20-fold higher towards human erythrocytes. Whereas 45 micrograms of the free cytotoxin/ml were needed for total haemolysis, the cytotoxic liposomes brought about the same effect at cytotoxin concentrations of 2-2.5 micrograms/ml, indicating the potential of the liposomes as a delivery system for the snake toxin.
Deregulated Expression of the Human Tumor Marker CEA and CEA Family Member CEACAM6 Disrupts Tissue Architecture and Blocks Colonocyte Differentiation (2002)

Human carcinoembryonic antigen (CEA) and the CEA family member CEACAM6 (formerly nonspecific cross-reacting antigen [NCA]) function in vitro, at least, as homotypic intercellular adhesion molecules and, in model systems, can block the terminal differentiation and anoikis of several different cell types. We have recently demonstrated that the increased cell surface levels of CEA and CEACAM6 in purified human colonocytes from freshly excised, well to poorly differentiated colon carcinomas are inversely correlated with the degree of cellular differentiation. Thus, deregulated expression of CEA/CEACAM6 could directly contribute to colon tumorigenesis by the inhibition of terminal differentiation and anoikis. Evidence against this view includes the common observation of increased CEA/CEACAM6 expression as normal colonocytes differentiate in their migration up colonic crypt walls. We report here the direct effects of deregulated overexpression of CEA/CEACAM6, at levels observed in colorectal carcinomas, on the differentiation of two human colonic cell lines, SW-1222 and Caco-2. Stable transfectants of both of these cell lines that constitutively express 10- to 30-fold higher cell surface levels of CEA/CEACAM6 than endogenous levels failed to polarize and differentiate into glandular structures in monolayer or 3D culture or to form colonic crypts in a tissue architecture assay in nude mice. In addition, these transfectants were found to exhibit increased tumorigenicity in nude mice. These results thus support the contention that deregulated overexpression of CEA and CEACAM6 could provide a tumorigenic contribution to colon carcinogenesis.
A gene duplication led to specialized γ‐aminobutyrate and β‐alanine aminotransferase in yeast (2007)

In humans, beta-alanine (BAL) and the neurotransmitter gamma-aminobutyrate (GABA) are transaminated by a single aminotransferase enzyme. Apparently, yeast originally also had a single enzyme, but the corresponding gene was duplicated in the Saccharomyces kluyveri lineage. SkUGA1 encodes a homologue of Saccharomyces cerevisiae GABA aminotransferase, and SkPYD4 encodes an enzyme involved in both BAL and GABA transamination. SkPYD4 and SkUGA1 as well as S. cerevisiae UGA1 and Schizosaccharomyces pombe UGA1 were subcloned, over-expressed and purified. One discontinuous and two continuous coupled assays were used to characterize the substrate specificity and kinetic parameters of the four enzymes. It was found that the cofactor pyridoxal 5'-phosphate is needed for enzymatic activity and alpha-ketoglutarate, and not pyruvate, as the amino group acceptor. SkPyd4p preferentially uses BAL as the amino group donor (V(max)/K(m)=0.78 U x mg(-1) x mm(-1)), but can also use GABA (V(max)/K(m)=0.42 U x mg(-1) x mm(-1)), while SkUga1p only uses GABA (V(max)/K(m)=4.01 U x mg(-1) x mm(-1)). SpUga1p and ScUga1p transaminate only GABA and not BAL. While mammals degrade BAL and GABA with only one enzyme, but in different tissues, S. kluyveri and related yeasts have two different genes/enzymes to apparently 'distinguish' between the two reactions in a single cell. It is likely that upon duplication approximately 200 million years ago, a specialized Uga1p evolved into a 'novel' transaminase enzyme with broader substrate specificity.
The use of the VerifyNow P2Y12 point-of-care device to monitor platelet function across a range of P2Y12 inhibition levels following prasugrel and clopidogrel administration (2008)

Variability in response to antiplatelet agents has prompted the development of point-of-care (POC) technology. In this study, we compared the VerifyNow P2Y12 (VN-P2Y12) POC device with light transmission aggregometry (LTA) in subjects switched directly from clopidogrel to prasugrel. Healthy subjects on aspirin were administered a clopidogrel 600 mg loading dose (LD) followed by a 75 mg/d maintenance dose (MD) for 10 days. Subjects were then switched to a prasugrel 60 mg LD and then 10 mg/d MD for 10 days (n = 16), or to a prasugrel 10 mg/d MD for 11 days (n = 19). Platelet function was measured by LTA and VN-P2Y12 at baseline and after dosing. Clopidogrel 600 mg LD/75 mg MD treatment led to a reduction in P2Y(12) reaction units (PRU) from baseline. A switch from clopidogrel MD to prasugrel 60 mg LD/10 mg MD produced an immediate decrease in PRU, while a switch to prasugrel 10 mg MD resulted in a more gradual decline. Consistent with the reduction in PRU, device-reported percent inhibition increased during both clopidogrel and prasugrel regimens. Inhibition of platelet aggregation as measured by LTA showed a very similar pattern to that found with VN-P2Y12 measurement, irrespective of treatment regimens. The dynamic range of VN-P2Y12 appeared to be narrower than that of LTA. With two different thienopyridines, the VN-P2Y12 device, within a somewhat more limited range, reflected the overall magnitude of change in aggregation response determined by LTA. The determination of the clinical utility of such POC devices will require their use in clinical outcome studies.
Real‐Time Blood Plasma Polymerase Chain Reaction for Management of Disseminated Adenovirus Infection (2003)

We evaluated the usefulness of quantifying blood plasma adenovirus DNA loads for the management of adenovirus infection. Quantification of adenovirus A, B, and C DNA loads was done with real-time polymerase chain reaction (PCR) assays. Blood plasma specimens obtained from 44 immunocompromised patients were screened prospectively with this method. PCR findings for 36 patients were negative, and none of the patients developed disseminated adenoviral disease. PCR findings for 8 patients were positive; all 8 had invasive adenoviral disease and were treated with cidofovir. Sequential measurements of adenovirus DNA loads were performed to monitor the effect of cidofovir therapy. Decrease in the blood plasma DNA load was significantly higher in patients with a good response to cidofovir than in patients with a poor response and was therefore correlated with survival. Detection of adenovirus DNA in blood plasma appears to be useful for identifying patients at risk for invasive disease. Moreover, quantification of adenovirus DNA loads in plasma is helpful for monitoring the efficacy of antiviral therapy.
O‐1057, a potent water‐soluble cannabinoid receptor agonist with antinociceptive properties (2000)

Cannabinoids have low water solubility, necessitating the use of a solubilizing agent. In this paper we investigated whether a novel water-soluble cannabinoid, 3-(5'-cyano-1', 1'-dimethylpentyl)-1-(4-N-morpholinobutyryloxy)-Delta(8)- tetrahydroca nnabinol hydrochloride (O-1057), would interact with cannabinoid receptors when water or saline were used as the only vehicle. O-1057 displaced [(3)H]-CP55940 from specific binding sites on Chinese hamster ovary (CHO) cell membranes expressing CB(1) or CB(2) cannabinoid receptors, with pK(i) values of 8.36 and 7.95 respectively. It also displaced [(3)H]-CP55940 from specific binding sites on rat brain membranes (pK(i) = 7.86). O-1057 inhibited forskolin-stimulated cyclic AMP production by both CB(1)- and CB(2)-transfected CHO cells (pEC(50) = 9.16 and 9.72 respectively), its potency matching that of CP55940 and exceeding that of Delta(9)-tetrahydrocannabinol. In the mouse isolated vas deferens, O-1057 inhibited electrically-evoked contractions with pEC(50) and E(max) values of 9.73 and 76.84% respectively. It was antagonized by 100 nM SR141716A, the pK(B) of SR141716A against O-1057 (8.90) approximating to that against CP55940 (8.97). O-1057 also behaved as a CB(1) receptor agonist in vivo, reducing mouse spontaneous activity and rectal temperature when injected intravenously and inducing antinociception in the mouse tail flick test when given intravenously (ED(50) = 0.02 mg kg(-1)), intrathecally, intracerebroventricularly or by gavage. In all these assays, O-1057 was more potent than Delta(9)-tetrahydrocannabinol and, at 0.1 mg kg(-1) i.v., was antagonized by SR141716A (3 mg kg(-1) i.v.). These data demonstrate the ability of the water-soluble cannabinoid, O-1057, to act as a potent agonist at CB(1) and CB(2) receptors and warrant investigation of the clinical potential of O-1057 as an analgesic.
Sequence-specific 2'5'-oligonucleotides in the molecular dissection of the biological activity of 2-5A. (1985)

Recently developed chemical synthetic methodology for facile preparation of sequence-specific 2'5'-oligonucleotides has allowed more exacting questions to be asked regarding the biological role of each of the nucleotide residues of 2-5A. We have found, employing analogs in which each adenosine residue has been sequentially replaced by adenosine (viz, ppp5'I2'p5'A2'p5'I, ppp5'A2'p5'I2'p5'A, ppp5'A2'p5'A2'p5'I) that the N6 amino group of the first (or 5'-terminal) adenosine residue of 2-5A trimer is critical in RNase L binding whereas the N6 amino moiety of the third (or 2'-terminal) adenosine residue of 2-5A is crucial for the activation of RNase L. The second or middle adenosine unit of 2-5A does not seem to be critical for either binding or activation. Similarly, in studies on sequence-specific tubercidin analogs of 2-5A, activation of but not binding to mouse RNase L was dependent on the presence of the purine N7 atoms of the first and third adenosine residues of 2-5A, but, as with the N6 amino group, the N7 moiety of the second adenosine residue of 2-5A was not essential for either binding to or activation of the 2-5A-dependent endonuclease. Finally, sequence-specific purine 8-bromination provided analogs of dramatically varying biological properties, and provided a 5'-monophosphate, p5'A2'p5'(br8A)2'p5'(br8A), which possessed 8% of the translational inhibitory action of 2-5A itself. This latter result may represent an important impetus toward obtaining a 2-5A derivative with biological activity in an intact cell.
Mapping Ligand Interactions with the Hyperpolarization Activated Cyclic Nucleotide Modulated (HCN) Ion Channel Binding Domain Using a Soluble Construct (2007)

Hyperpolarization activated cyclic nucleotide modulated (HCN) ion channel currents are activated by hyperpolarization and modulated in response to changes in cytosolic adenosine 3',5'-cyclic monophosphate (cAMP) concentrations. A cDNA chimera combining the rat HCN2 cyclic nucleotide binding domain and the DNA binding domain of the cAMP receptor protein (CRP) from E. coli and the histidine tag (HCN2/CRP) was expressed and purified. The construct is capable of forming only non-ligand dependent dimers because the C-linker region of the channel is not present in this construct. The construct binds 8-[[2-[(fluoresceinylthioureido) amino] ethyl] thio] adenosine-3',5'-cyclic monophosphate (8-fluo cAMP) with a Kd of 0.299 microM as determined with a monomer binding model. The Ki values of 20 ligands related to cAMP were measured in order to determine the properties necessary for a ligand to bind to the HCN2 binding domain. This is the first report of cAMP and gunaosine 3',5'-cyclic monophosphate (cGMP) affinities to the HCN2 binding domain being equivalent, even though they modulate the channel with a 10-fold difference in K0.5. Furthermore, the array of ligands measured allows the preference rank order for each purine ring position to be determined: position 1, H > NH2 > O; position 2, NH2 > Cl > H > O; position 6, NH2 > Cl > H > O; and position 8, NH2 > Cl > H > O. Finally, the ability of HCN2/CRP to bind cyclic nucleotide pyrimidine rings at concentrations approximately 1.33 times greater than cAMP suggests that ribofuranose is key for binding.
Identification of human neutralization-inducing regions of the human immunodeficiency virus type 1 envelope glycoproteins. (1992)

Four major neutralizing regions of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein were identified and characterized with a panel of 80 HIV-1 antibody-positive human sera. Levels of neutralizing antibodies against the HIV-1 strains IIIB, SF2, and RF were compared with reactivity in ELISAs against peptides that correspond to certain regions of the HIV-1 envelope. A correlation between high neutralizing activity and strong seroreactivity against specific peptides suggested that the corresponding regions might be involved in neutralization. This was further substantiated by using peptides to inhibit neutralization by a panel of 10 HIV-1 antibody-positive sera. The positions of three neutralizing sites, defined earlier mostly by antisera from animals, were confirmed in the present study. Human sera thus recognize the strain-specific third variable region of gp120 (amino acids 304-318), the C-terminal end of gp120 (amino acids 489-508), and the conserved region in the intracellular part of gp41 (amino acids 732-746). It is likely that these different regions mediate help rather than self-sufficient neutralization. Furthermore, a human neutralizing region was detected in a conserved part of gp41 (amino acids 647-671). Accordingly, neutralizing antibodies directed to this region were found to be cross-reactive between HIV-1 strains. Peptides corresponding to these four regions were able to inhibit neutralization mediated by serum from HIV-1 antibody-positive individuals. These results indicate that this conserved B-cell epitope of the HIV-1 envelope elicits a virus-neutralizing antibody response during natural infection in humans and may therefore be considered for inclusion in a vaccine against HIV-1.
Human xanthine oxidase converts nitrite ions into nitric oxide (NO) (1997)

Conference Article| August 01 1997 Human xanthine oxidase converts nitrite ions into nitric oxide (NO) Zhi Zhang; Zhi Zhang Search for other works by this author on: This Site PubMed Google Scholar Declan P. Naughton; Declan P. Naughton Search for other works by this author on: This Site PubMed Google Scholar David R. Blake; David R. Blake Search for other works by this author on: This Site PubMed Google Scholar Nigel Benjamin; Nigel Benjamin 1Bone and Joint Research Unit, Department of Clinical Pharmacology, St. Bartholomew's and the Royal London School of Medicine and Dentistry, 25–29 Ashfield Street, London E1 2AD, UK Search for other works by this author on: This Site PubMed Google Scholar Cliff R. Stevens; Cliff R. Stevens Search for other works by this author on: This Site PubMed Google Scholar Paul G. Winyard; Paul G. Winyard Search for other works by this author on: This Site PubMed Google Scholar Martyn C.R. Symons; Martyn C.R. Symons Search for other works by this author on: This Site PubMed Google Scholar Roger Harrison Roger Harrison 2Bone and Joint Research Unit, School of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1997) 25 (3): 524S. https://doi.org/10.1042/bst025524s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation Zhi Zhang, Declan P. Naughton, David R. Blake, Nigel Benjamin, Cliff R. Stevens, Paul G. Winyard, Martyn C.R. Symons, Roger Harrison; Human xanthine oxidase converts nitrite ions into nitric oxide (NO). Biochem Soc Trans 1 August 1997; 25 (3): 524S. doi: https://doi.org/10.1042/bst025524s Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu nav search search input Search input auto suggest search filter All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1997 Biochemical Society1997 Article PDF first page preview Close Modal You do not currently have access to this content.
Prediction of protein-protein interaction types using association rule based classification (2009)

The advantage of our approach is that we can extract biologically significant information from the interpretation of the discovered association rules in terms of understandability and interpretability of rules. A web application based on our method can be found at http://bioinfo.ssu.ac.kr/~shpark/picasso/
Novel MT1-MMP Small-Molecule Inhibitors Based on Insights into Hemopexin Domain Function in Tumor Growth (2012)

Membrane type-1 matrix metalloproteinase (MT1-MMP) is a promising drug target in malignancy. The structure of MT1-MMP includes the hemopexin domain (PEX) that is distinct from and additional to the catalytic domain. Current MMP inhibitors target the conserved active site in the catalytic domain and, as a result, repress the proteolytic activity of multiple MMPs instead of MT1-MMP alone. In our search for noncatalytic inhibitors of MT1-MMP, we compared the protumorigenic activity of wild-type MT1-MMP with an MT1-MMP mutant lacking PEX (ΔPEX). In contrast to MT1-MMP, ΔPEX did not support tumor growth in vivo, and its expression resulted in small fibrotic tumors that contained increased levels of collagen. Because these findings suggested an important role for PEX in tumor growth, we carried out an inhibitor screen to identify small molecules targeting the PEX domain of MT1-MMP. Using the Developmental Therapeutics Program (National Cancer Institute/NIH), virtual ligand screening compound library as a source and the X-ray crystal structure of PEX as a target, we identified and validated a novel PEX inhibitor. Low dosage, intratumoral injections of PEX inhibitor repressed tumor growth and caused a fibrotic, ΔPEX-like tumor phenotype in vivo. Together, our findings provide a preclinical proof of principle rationale for the development of novel and selective MT1-MMP inhibitors that specifically target the PEX domain.