gebhart/patrepeval huggingface dataset:
Enzymes work by solvation substitution rather than by desolvation. (1989)

Considerable attention has recently been drawn to the hypothesis that enzymes catalyze their reactions by displacing solvent and creating an environment similar to the gas phase for the reacting substrates. This "desolvation hypothesis" is reexamined in this paper by defining a common reference energy for reactions in various environments. It is argued that consistent attempts to describe the actual energetics of enzymatic reactions, taking either gas phase or solution as a reference, would contradict the above hypothesis. That is, the enzyme does remove water molecules from its substrate, but substitutes these molecules for another polar environment (namely, its active site). By taking amide hydrolysis as an example, we use experimentally estimated solvation energies and analyze the reaction profile in the gas phase, in solution, and in enzyme active sites. We show that the gas-phase reaction is characterized by an enormous activation barrier (associated with forming the charged nucleophile from neutral fragments), although the nucleophilic attack is essentially barrierless. On the other hand, the enzyme and solution reactions are found to have similar reaction profiles, with a lower activation barrier for the enzymatic reaction. Presumably, the fact that previous analyses of this problem did not involve the construction of the relevant thermodynamic cycles (and quantitative estimates of the corresponding solvation energies) led to the desolvation hypothesis. Our conclusion is that enzyme active sites provide specific polar environments that do not resemble the gas phase but that are designed for electrostatic stabilization of ionic transition states and that "solvate" these states more than water does.
The role of erythropoietin, megakaryocyte colony-stimulating factor, and T-cell-derived factors on human megakaryocyte colony formation: evidence for T-cell-mediated and T-cell-independent stem cell proliferation. (1987)

Recent studies suggest that megakaryocytopoiesis is governed by a dual-level regulatory process, with megakaryocyte colony-stimulating factor (Meg-CSF) primarily influencing proliferation of the committed precursors and thrombopoietin required for megakaryocyte ploidy amplification and for maturation. The authors have examined different sources of Meg-CSF in a microagar culture system with a view to their capacity to enhance megakaryocyte colony formation directly or via an indirect T-lymphocyte- or monocyte-mediated effect. The comparative influences of phytohemagglutinin-stimulated leukocyte-conditioned medium (PHA-LCM), erythropoietin (Epo), sera of patients with severe aplastic anemia, and direct PHA addition to the culture were evaluated for their capacity to enhance megakaryocytic colony formation as well as for the maturation rate of megakaryocytes (Mk) grown in our microagar culture system. Each treatment by itself enhanced colony formation from unseparated low-density cells. Removal of T-lymphocytes and monocytes from the bone marrow sample caused a cessation of the enhancing effect of direct PHA addition to cultures stimulated with Epo, but did not influence the enhancing activities of severe aplastic anemia serum (SAA), PHA-LCM, and Epo. The results show that SAA serum, Epo, and PHA-LCM induced Mk colony formation directly and therefore may act via a common mechanism. Differences, however, were observed concerning their colony-stimulating potency and their influence on the Mk maturation rate.
The effect of interleukin-1beta (IL-1beta) and tumor necrosis factor-alpha (TNF-alpha) on granulocyte macrophage-colony stimulating factor (GM-CSF) production by neuronal precursor cells. (2002)

IL-1beta and TNF-alpha both increase GM-CSF mRNA expression by NT2 cells, but only IL-1beta increases net GM-CSF protein accumulation.
Sequence Dependent Effects of CpG Cytosine Methylation. A Joint 1H-NMR and 31P-NMR Study (1995)

The impact of cytosine methylation in the central CpG step of two closely related octanucleotide duplexes d(CATCGATG)2 and d(CTTCGAAG)2 was examined by 1H-NMR and 31P-NMR experiments, and a quantitative structural analysis was performed using the NOE-derived distances, the sugar puckers and the ε torsion angles. The two starting oligonucleotides displayed a B-DNA conformation with, however, significant local structure differences. Although the methylated oligonucleotides retained their B-DNA conformation, different structural and thermal stability effects were observed. The magnitude of the methylation effects was to depend on the initial conformation of the CpG site, which is governed by the nature of the dinucleotide AT or TT located on the CpG flanks. As an example of sequence dependence, the methylation of CpG entailed larger conformational variation in d(CATCGATG)2 than in d(CTTCGAAG)2. In this study, the 1H and 31P chemical-shift parameters averred as extremely sensitive probes for detecting subtle conformational changes. Finally, our comparative results may aid our understanding of the structural and related biological effects produced by cytosine methylation in DNA.
Crystal Structures of HIV-1 Reverse Transcriptase in Complex with Carboxanilide Derivatives, (1998)

The carboxanilides are nonnucleoside inhibitors (NNIs) of HIV-1 reverse transcriptase (RT), of potential clinical importance. The compounds differ in potency and in their retention of potency in the face of drug resistance mutations. Whereas UC-84, the prototype compound, only weakly inhibits many RTs bearing single point resistance mutations, inhibition by UC-781 is little affected. It has been proposed that UC-38 and UC-781 may form quaternary complexes with RT at a site other than the known binding pocket of other NNIs. X-ray crystal structures of four HIV-1 RT-carboxanilide complexes (UC-10, UC-38, UC-84, and UC-781) reported here reveal that all four inhibitors bind in the usual NNI site, forming binary 1:1 complexes with RT in the absence of substrates with the amide/thioamide bond in cis conformations. For all four complexes the anilide rings of the inhibitors overlap aromatic rings of many other NNIs bound to RT. In contrast, the second rings of UC-10, UC-84, and UC-781 do not bind in equivalent positions to those of other "two-ring" NNIs such as alpha-APA or HEPT derivatives. The binding modes most closely resemble that of the structurally dissimilar NNI, Cl-TIBO, with a common hydrogen bond between each carboxanilide NH- group and the main-chain carbonyl oxygen of Lys101. The binding modes differ slightly between the UC-10/UC-781 and UC-38/UC-84 pairs of compounds, apparently related to the shorter isopropylmethanoyl substituents of the anilide rings of UC-38/UC-84, which draws these rings closer to residues Tyr181 and Tyr188. This in turn explains the differences in the effect of mutated residues on the binding of these compounds.
Demonstration of membrane receptors for human natural and recombinant 125I‐labeled tumor necrosis factor on HeLa cell clones and their role in tumor cell sensitivity (1986)

Samples of natural and recombinant tumor necrosis factor (TNF) were labelled with 125I by use of Iodobeads and were used to study TNF receptor expression on different HeLa clones. Both labeled preparations retained cytotoxic activity after 125I-labelling and were indistinguishable from their unlabeled counterparts on sodium dodecylsulfate/polyacrylamide gel electrophoresis. They bound specifically to TNF-sensitive cells but not to HeLa clones that were resistant to TNF. The binding of 125I-TNF was competed up to 90% by the addition of non-radiolabeled TNF. The binding reached a half-maximal level at 10 pM and saturation at 100 pM. These concentrations approximated those required for cell destruction. Scatchard analysis of the binding data yielded linear plots suggesting that TNF binds to homogeneous TNF receptor sites. The number of receptor sites ranged between 770 and 2200 sites on TNF-sensitive cells. The surface expression of these TNF receptors appeared to be necessary but not sufficient for the cells to become sensitive against the cytotoxic action of TNF. One of the HeLa clones was found to express the same number of TNF receptors as the most sensitive clone, but was nevertheless resistant to the toxic effect of TNF.
A Capillary Array Gel Electrophoresis System Using Multiple Laser Focusing for DNA Sequencing (1996)

A very simple and highly sensitive capillary array gel electrophoresis system is constructed to analyze DNA fragments. On-column detection of DNA migration in a large number of gel-filled capillaries is carried out using side-entry laser irradiation and with a CCD camera, although it has been considered impossible because the irradiation laser is scattered strongly at the surfaces of the first few capillaries. By optimizing optical conditions, the laser beam can be focused repeatedly to irradiate all the capillaries held on a plate by working each capillary as a cylindrical convex lens. DNA sequencing samples migrating in 24 capillaries can simultaneously be analyzed with the system.
Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA (2014)

Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.
Season of Birth: Schizophernia and Bipolar Disorder (1986)

Studies investigating the association between the risk of schizophrenia and season of birth are reviewed and the association clearly established. This association cannot be explained on the basis of age-incidence or age-prevalence artifacts. Other studies suggest there may be an association between bipolar disorder and season of birth. The leading theory in explaining the season of birth phenomenon is that a seasonal factor (such as viral infection, malnutrition, vitamin deficiency, prenatal or obstetrical complications, or ambient temperature) can damage an infant's brain and thereby predispose the child to later development of psychosis. Evidence suggests that the seasonal effect is associated with a subgroup of schizophrenics who have early onset of psychosis, less genetic loading than other schizophrenics, and better prognosis. Case-control studies are needed comparing winterborn to nonwinter-born schizophrenics.
Novel Oligoamine Analogues Inhibit Lysine-Specific Demethylase 1 and Induce Reexpression of Epigenetically Silenced Genes (2009)

The use of LSD1-inhibiting oligoamine analogues in combination with DNA methyltransferase inhibitors represents a highly promising and novel approach for epigenetic therapy of cancer.
Chronic hypoxia augments depolarization-induced Ca2+sensitization in pulmonary vascular smooth muscle through superoxide-dependent stimulation of RhoA (2009)

Rho kinase (ROCK)-dependent vasoconstriction has been implicated as a major factor in chronic hypoxia (CH)-induced pulmonary hypertension. This component of pulmonary hypertension is associated with arterial myogenicity and increased vasoreactivity to receptor-mediated agonists and depolarizing stimuli resulting from ROCK-dependent myofilament Ca(2+) sensitization. On the basis of separate lines of evidence that CH increases pulmonary arterial superoxide (O(2)(-)) generation and that O(2)(-) stimulates RhoA/ROCK signaling in vascular smooth muscle (VSM), we hypothesized that depolarization-induced O(2)(-) generation mediates enhanced RhoA-dependent Ca(2+) sensitization in pulmonary VSM following CH. To test this hypothesis, we determined effects of the ROCK inhibitor HA-1077 and the O(2)(-)-specific spin trap tiron on vasoconstrictor reactivity to depolarizing concentrations of KCl in isolated lungs and Ca(2+)-permeabilized, pressurized small pulmonary arteries from control and CH (4 wk at 0.5 atm) rats. Using the same vessel preparation, we examined effects of CH on KCl-dependent VSM membrane depolarization and O(2)(-) generation using sharp electrodes and the fluorescent indicator dihydroethidium, respectively. Finally, using a RhoA-GTP pull-down assay, we investigated the contribution of O(2)(-) to depolarization-induced RhoA activation. We found that CH augmented KCl-dependent vasoconstriction through a Ca(2+) sensitization mechanism that was inhibited by HA-1077 and tiron. Furthermore, CH caused VSM membrane depolarization that persisted with increasing concentrations of KCl, enhanced KCl-induced O(2)(-) generation, and augmented depolarization-dependent RhoA activation in a O(2)(-)-dependent manner. These findings reveal a novel mechanistic link between VSM membrane depolarization, O(2)(-) generation, and RhoA activation that mediates enhanced myofilament Ca(2+) sensitization and pulmonary vasoconstriction following CH.
Redefining cholesterol's role in the mechanism of the cholesterol-dependent cytolysins (2003)

The cholesterol-dependent cytolysins (CDCs) constitute a large family of pore-forming toxins that function exclusively on cholesterol-containing membranes. A detailed analysis of the various stages in the cytolytic mechanism of three members of the CDC family revealed that significant depletion of cholesterol from the erythrocyte membrane stalls these toxins in the prepore complex. Therefore, the depletion of membrane cholesterol prevents the insertion of the transmembrane beta-barrel and pore formation. These unprecedented findings provide a paradigm for the involvement of cholesterol in the CDC cytolytic mechanism and that of other pore-forming toxins whose activity is enhanced by the presence of membrane cholesterol.
The Future of Fracturing-Fluid Technology and Rates of Hydrocarbon Recovery (2008)

Abstract A high percentage of oil and gas wells worldwide are hydraulically fractured in order to allow a reservoir to become economically producible and to improve the rate of hydrocarbon production. Annual global investments for hydraulic fracturing are at one billion dollars. Crosslinked polymer fluids are the most commonly used fracturing fluid because of cost and performance criteria. The crosslinked polymer fluids exhibit exceptional performance features to initiate and propagate a fracture, carry proppant and control fluid leak-off into the reservoir during a treatment. However, crosslinked polymer fluids leave a significant amount of polymeric filtercake material in the fracture once a treatment is completed. Decades of improving oxidative, enzyme and other breakers for the polymer fluids has only marginally improved from about 30% to about 50% by weight the amount of polymer residue left within the fracture. The result has been a continuation of much lower than optimum hydrocarbon recovery rates for many wells. New surfactant-based fluid technology is being developed that will in many geographic regions replace polymeric-based fracturing fluids over the next decade. This paper will introduce a new fluid technology that uses nanoparticles, special internal breakers and low molecular weight viscoelastic surfactants (VES) to achieve the performance features of crosslinked polymer fluids but leaves little to no gel residue. Unique nanoparticles have been found that "pseudo-crosslink" VES micelles together through electrostatic and van der Waals forces. This micelle-networked fluid property will allow unique "pseudo-filtercake" to form on porous media, like crosslinked polymer fluids exhibit, to control fluid leak-off and improve fluid efficiency. The special internal breakers reside within the micelles and go wherever the fluid goes, including the networked micelles composing the pseudo-filtercake. The internal breakers controllably break the viscosity of the VES-based pseudo-filtercake by rearranging the VES micelles to spherical non-viscous structures and dispersed nanoparticles that readily flow back with producing fluids and do not impair the proppant pack conductivity. The primary result will allow a wide range of hydraulically fractured reservoirs to produce at substantially higher sustained rates than presently achievable, particularly for deepwater and other high investment wells.
Ligation of cancer cell surface GRP78 with antibodies directed against its COOH-terminal domain up-regulates p53 activity and promotes apoptosis (2009)

Binding of activated α(2)-macroglobulin to GRP78 on the surface of human prostate cancer cells promotes proliferation by activating signaling cascades. Autoantibodies directed against the activated α(2)-macroglobulin binding site in the NH(2)-terminal domain of GRP78 are receptor agonists, and their presence in the sera of cancer patients is a poor prognostic indicator. We now show that antibodies directed against the GRP78 COOH-terminal domain inhibit [(3)H]thymidine uptake and cellular proliferation while promoting apoptosis as measured by DNA fragmentation, Annexin V assay, and clonogenic assay. These antibodies are receptor antagonists blocking autophosphorylation and activation of GRP78. Using 1-LN and DU145 prostate cancer cell lines and A375 melanoma cells, which express GRP78 on their cell surface, we show that antibodies directed against the COOH-terminal domain of GRP78 up-regulate the tumor suppressor protein p53. By contrast, antibody directed against the NH(2)-terminal domain of GRP78 shows negligible effects on p53 expression. PC-3 prostate cancer cells, which do not express GRP78 on their cell surface, are refractory to the effects of anti-GRP78 antibodies directed against either the COOH- or NH(2)-terminal domains. However, overexpression of GRP78 in PC-3 cells causes translocation of GRP78 to the cell surface and promotes apoptosis when these cells are treated with antibody directed against its COOH-terminal domain. Silencing GRP78 or p53 expression by RNA interference significantly blocked the increase in p53 induced by antibodies. Antibodies directed against the COOH-terminal domain may play a therapeutic role in cancer patients whose tumors trigger the production of autoantibodies directed against the NH(2)-terminal domain of GRP78.
A content-based resource location mechanism in PeerIS (2003)

With the flurry of research on P2P computing, many P2P technical challenges have emerged, one of which is how to efficiently locate desired resources. Advances have been made in this hot research field, where the pioneers are Pastry, CAN, Chord, and Tapestry. By using the functionality of a distributed hash table, they have achieved fair effectiveness. However they have many common limitations, such as ignoring the autonomous nature of peers, and just supporting weakly semantic functions. According to reality in the distributed network, we propose a content-based location mechanism, which not only keeps the autonomy of peers, but also supports approximate query and finer granularity of content sharing. Furthermore, this mechanism also facilitates P2P system to evolve dynamically. We have also used PeerIS, a P2P based information system used to verify it and obtained satisfactory results.
Interplay of microRNAs, transcription factors and target genes: linking dynamic expression changes to function (2013)

MicroRNAs (miRNAs) are ubiquitously expressed small non-coding RNAs that, in most cases, negatively regulate gene expression at the post-transcriptional level. miRNAs are involved in fine-tuning fundamental cellular processes such as proliferation, cell death and cell cycle control and are believed to confer robustness to biological responses. Here, we investigated simultaneously the transcriptional changes of miRNA and mRNA expression levels over time after activation of the Janus kinase/Signal transducer and activator of transcription (Jak/STAT) pathway by interferon-γ stimulation of melanoma cells. To examine global miRNA and mRNA expression patterns, time-series microarray data were analysed. We observed delayed responses of miRNAs (after 24-48 h) with respect to mRNAs (12-24 h) and identified biological functions involved at each step of the cellular response. Inference of the upstream regulators allowed for identification of transcriptional regulators involved in cellular reactions to interferon-γ stimulation. Linking expression profiles of transcriptional regulators and miRNAs with their annotated functions, we demonstrate the dynamic interplay of miRNAs and upstream regulators with biological functions. Finally, our data revealed network motifs in the form of feed-forward loops involving transcriptional regulators, mRNAs and miRNAs. Additional information obtained from integrating time-series mRNA and miRNA data may represent an important step towards understanding the regulatory principles of gene expression.
Proton NMR Assignments and Solution Conformation of RANTES, a Chemokine of the C-C Type (1995)

1H NMR has been used to investigate the structural properties of RANTES, a protein from the C-C branch of the chemotactic cytokine family that has a strong chemoattractive effect on monocytes, lymphocytes, and eosinophils. Titration of pH from 5.0 to 2.5 indicates that RANTES is extensively aggregated in solution above pH 4.0. At pH 3.7 the protein is mostly dimeric, although this species does dissociate to the monomer with a Kd of 35 microM. NMR data have been acquired and resonance assignments made for the dimeric species. Structures of the dimer have been generated by distance geometry and simulated annealing calculations that utilized 1956 intramolecular distance restraints, 120 intermolecular distance restraints, 164 dihedral angle restraints, and 68 restraints enforcing 34 hydrogen bonds (17.0 restraints per residue). The structure is well-defined (average root mean square deviation from the average structure of 0.38 +/- 0.06 and 0.53 +/- 0.12 A for backbone heavy atoms of residues 4-66 of the monomer and dimer, respectively). Each monomer consists of a C-terminal alpha-helix packing against a three-stranded antiparallel beta-sheet and two short N-terminal beta-strands; dimerization occurs between the N-terminal regions of each monomer. This quaternary structure is very different from that of the C-X-C chemokines such as interleukin-8 and melanoma growth stimulatory activity but similar to that found for the C-C chemokine macrophage inflammatory factor 1 beta. Distinct structural differences between RANTES and other chemokines at both the tertiary and quaternary level are discussed with regard to the distinct biological functions of the C-C and C-X-C members of this protein family.