gebhart/patrepeval huggingface dataset:
Isolation and analysis of the gene encoding the pyruvate-ferredoxin oxidoreductase of Desulfovibrio africanus, production of the recombinant enzyme in Escherichia coli, and effect of carboxy-terminal deletions on its stability (1997)

Previous studies have shown that the pyruvate-ferredoxin oxidoreductase (POR) of the sulfate-reducing bacterium Desulfovibrio africanus is a homodimer that contains one thiamine pyrophosphate and three [4Fe-4S]2+/1+ centers/subunit. Interestingly, the enzyme isolated from a strictly anaerobic bacterium is highly stable in the presence of oxygen, in contrast to the other PORs characterized in anaerobic organisms (L. Pieulle, B. Guigliarelli, M. Asso, F. Dole, A. Bernadac, and E. C. Hatchikian, Biochim. Biophys. Acta 1250:49-59, 1995). We report here the determination of the nucleotide sequence of the por gene encoding the D. africanus POR. The amino acid sequence deduced from this nucleotide sequence corresponds to the first primary structure of a homodimeric POR from strictly anaerobic bacteria. The subunit of the D. africanus POR contains two ferredoxin-type [4Fe-4S] cluster binding motifs (CX2CX2CX3CP) and four additional highly conserved cysteines belonging to a nontypical motif. These 12 cysteine residues may coordinate the three Fe-S centers present in D. africanus POR. The thiamine pyrophosphate binding domain is located in the C-terminal part of the protein close to the four conserved cysteine residues. The D. africanus enzyme sequence appears homologous to the other POR sequences. However, the enzyme differs from all other PORs by a C-terminal extension of about 60 residues of its polypeptide chain. The two cysteine residues located in this additional region may be involved in the formation of a disulfide bridge associated with the activation process of the catalytic activity. The por gene has been expressed, for the first time, in anaerobically grown Escherichia coli behind the isopropyl-beta-D-thiogalactopyranoside-inducible tac promoter, resulting in the production of POR in its active form. The recombinant enzyme is stable toward oxygen during several days, and initial characterization of the recombinant POR showed that its activity increased in the presence of dithioerythritol. These properties indicate that the recombinant POR behaves like the native D. africanus enzyme. The study of carboxy-terminal deletion mutants strongly suggests that deletions in the C-terminal region of D. africanus enzyme can have dramatic effects on the stability of the enzyme toward oxygen.
The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores (2004)

A hydrophobic constriction site can act as an efficient barrier to ion and water permeation if its diameter is less than the diameter of an ion's first hydration shell. This hydrophobic gating mechanism is thought to operate in a number of ion channels, e.g. the nicotinic receptor, bacterial mechanosensitive channels (MscL and MscS) and perhaps in some potassium channels (e.g. KcsA, MthK and KvAP). Simplified pore models allow one to investigate the primary characteristics of a conduction pathway, namely its geometry (shape, pore length, and radius), the chemical character of the pore wall surface, and its local flexibility and surface roughness. Our extended (about 0.1 micros) molecular dynamic simulations show that a short hydrophobic pore is closed to water for radii smaller than 0.45 nm. By increasing the polarity of the pore wall (and thus reducing its hydrophobicity) the transition radius can be decreased until for hydrophilic pores liquid water is stable down to a radius comparable to a water molecule's radius. Ions behave similarly but the transition from conducting to non-conducting pores is even steeper and occurs at a radius of 0.65 nm for hydrophobic pores. The presence of water vapour in a constriction zone indicates a barrier for ion permeation. A thermodynamic model can explain the behaviour of water in nanopores in terms of the surface tensions, which leads to a simple measure of 'hydrophobicity' in this context. Furthermore, increased local flexibility decreases the permeability of polar species. An increase in temperature has the same effect, and we hypothesize that both effects can be explained by a decrease in the effective solvent-surface attraction which in turn leads to an increase in the solvent-wall surface free energy.
Conformation-specific monoclonal antibodies to the calcium-induced structure of protein C. (1986)

Monoclonal antibodies to various domains of human protein C were characterized, and the cross-reactivity of these antibodies with other vitamin K-dependent proteins was explored. Three antibodies, JTC-1, -2, and -3 reacted with protein C only in the presence of Ca2+ and were shown to bind to the light chain of protein C. It is suggested that these antibodies recognize a gamma-carboxyglutamic acid domain-related conformational change induced by metal ions, evidenced by the fact that half-maximal binding was observed at calcium concentration of 0.5, 0.6, and 0.7 mM, respectively, by the fact that these antibodies, even in the presence of Ca2+, do not react with gamma-carboxyglutamic acid domainless protein C, and by the fact that Zn2+ and Tb3+ support binding in essentially the same way. Each cell line was stabilized by recloning five times. In addition each antibody had a single isoelectric point and was of the IgG1 kappa class. The interaction of antibodies JTC-1, -2; and -3 with protein C-Ca2+ was characterized by a single class of binding sites with Kd of 3.98 X 10(-9) M, 4.01 X 10(-9) M, and 6.76 X 10(-9) M, respectively. However, antibodies JTC-1, -2, and -3 bound to prothrombin-Ca2+ with Kd of 7.81 X 10(-9) M, 2.0 X 10(-7) M, and higher than 1.0 X 10(-5) M, respectively. In addition they had weak affinity for factor X in the presence of Ca2+. The results indicate that the antibodies JTC-1, -2, and -3 are conformation-specific monoclonal antibodies directed against an at least partially common metal ion-induced three-dimensional structure in protein C, prothrombin, and factor X.
Colloidal Organohalide Perovskite Nanoplatelets Exhibiting Quantum Confinement (2015)

We prepare colloidal nanoplatelets of methylammonium lead bromide (MAPbBr3) perovskite and compare the optical signatures of excitons in these two-dimensional systems to spherical perovskite nanocrystals and the corresponding bulk phase. We find that excitonic features that had previously been attributed to quantum confinement in MAPbBr3 nanocrystals are in fact a property of the bulk perovskite phase. Furthermore, we find that higher-energy absorption features originate from two-dimensional nanoplatelets, which are present in the nanocrystal reaction product. Upon further purification, we obtain colloidal nanoplatelets with predominantly single unit cell thickness and submicron lateral dimensions, which are stable in solution and exhibit a sharp excitonic absorption feature 0.5 eV blue-shifted from that of the three-dimensional bulk MAPbBr3 phase, representing a new addition to the growing family of colloidal two-dimensional nanostructures.
NMR Structure of the [2Fe-2S] Ferredoxin Domain from Soluble Methane Monooxygenase Reductase and Interaction with Its Hydroxylase, (2001)

The soluble methane monooxygenase (sMMO) from Methylococcus capsulatus (Bath) is a multicomponent enzyme system required for the conversion of methane to methanol. It comprises a hydroxylase, a regulatory protein, and a reductase. The reductase contains two domains: an NADH-binding and FAD-containing flavin domain and a ferredoxin (Fd) domain carrying a [2Fe-2S] cofactor. Here, we report the solution structure of the reduced form of the 98-amino acid Fd domain (Blazyk, J. L., and Lippard, S. J. Unpublished results) determined by nuclear magnetic resonance (NMR) spectroscopy and restrained molecular dynamics calculations. The structure consists of six beta strands arranged into two beta sheets as well as three alpha helices. Two of these helices form a helix-proline-helix motif, unprecedented among [2Fe-2S] proteins. The [2Fe-2S] cluster is coordinated by the sulfur atoms of cysteine residues 42, 47, 50, and 82. The 10.9 kDa ferredoxin domain of the reductase protein transfers electrons to carboxylate-bridged diiron centers in the 251 kDa hydroxylase component of sMMO. The binding of the Fd domain with the hydroxylase was investigated by NMR spectroscopy. The hydroxylase binding surface on the ferredoxin protein has a polar center surrounded by patches of hydrophobic residues. This arrangement of amino acids differs from that by which previously studied [2Fe-2S] proteins interact with their electron-transfer partners. The critical residues on the Fd domain involved in this binding interaction map well onto the universally conserved residues of sMMO enzymes from different species. We propose that the [2Fe-2S] domains in these other sMMO systems have a fold very similar to the one found here for M. capsulatus (Bath) MMOR-Fd.
ChemInform Abstract: STUDIES ON LACTAMS. XLVI. BETA‐LACTAMS AS SYNTHONS. SYNTHESIS OF HETEROCYCLES VIA BETA‐LACTAM CLEAVAGE (1977)

Abstract 37 Lit.‐Stellen werden in einer Untersuchung über die Synthese von Heterocyclen über eine β‐Lactam‐Spaltung ausgewertet.
Purification and characterization of a GTP-pyrophosphate exchange activity from vaccinia virions. Association of the GTP-pyrophosphate exchange activity with vaccinia mRNA guanylyltransferase . RNA (guanine-7-)methyltransferase complex (capping enzyme). (1980)

A core-associated enzyme, which catalyzes a nucleotide-pyrophosphate exchange with GTP, has been purified from vaccinia virions. The enzyme requires MgCl2 for activity, has an alkaline pH optimum, and specifically utilizes GTP as the exchanging nucleotide. The enzyme does not catalyze exchange of GMP with GTP. The GTP-PPi exchange enzyme co-purifies with vaccinia capping enzyme (RNA guanylyltransferase and RNA (guanine-7-)methyltransferase) through successive chromatography steps on DEAE-cellulose, DNA-cellulose, and phosphocellulose. GTP-PPi exchange and capping activities remain physically associated during sedimentation in a glycerol gradient. Under high salt conditions (1 M NaCl), GTP-PPi exchange, capping, and methylating activities co-sediment with an RNA triphosphatase activity and a nucleoside triphosphate phosphohydrolase activity as a 6.5 S multifunctional enzyme complex which contains two major polypeptides of 96,000 and 26,000 molecular weight. The characteristics of the various enzymatic reactions catalyzed by this complex are described. The GTP-PPi exchange reaction of vaccinia guanylyltransferase affords a simple, sensitive assay for capping enzyme function. The relevance of the GTP-PPi exchange reaction to the mechanism of transguanylylation is considered.
Surface and Chemical Study of SiO2·P2O5·CaO·(MgO) Bioactive Glasses (2000)

Glasses in SiO2·CaO·P2O5 and SiO2·CaO·P2O5·MgO systems have been prepared by a sol−gel synthesis procedure. The calcined glasses have been characterized by XRD, N2 adsorption, Hg porosimetry, XPS and TEM and have been also subjected to in vitro tests (immersion in a simulated body fluid) to evaluate their bioactivity. The presence of magnesium in the glasses increases the surface area and porosity, but it retards the formation of an apatite layer on the surface of glasses in the in vitro test. The XPS reveals that the surfaces of the glasses are richer in phosphorus and poorer in calcium than the bulk, whereas the magnesium, if present, associates preferentially to phosphorus at the glass surface. The TEM shows the presence of apatite-like calcium phosphate domains in the magnesium-free glasses, which are barely detected in the glasses, which contain this element. These apatitic domains are proposed to be the nucleation centers for the crystallization of apatite in the in vitro tests.
Chemopreventive effects of lupulone, a hop β-acid, on human colon cancer-derived metastatic SW620 cells and in a rat model of colon carcinogenesis (2007)

The bitter acids of hops (Humulus lupulus L.) mainly consist of humulones or alpha-acids and lupulones or beta-acids. We aimed to evaluate the antiproliferative mechanisms of lupulones on a human metastatic colon carcinoma-derived cell line (SW620 cells) and to assess their chemopreventive effects in a model of colon carcinogenesis. SW620 cell growth was inhibited by 70% after a 48 h exposure to lupulones (40 microg/ml). Lupulones up-regulated the expression of Fas receptor (Fas) and Fas ligand (FasL) as well as TNF-related apoptosis inducing ligand (TRAIL)-R1 (DR4) and -R2 (DR5) receptor proteins, suggesting the involvement of Fas and TRAIL receptors-mediated pathways in lupulone-induced apoptosis. Lupulones also increased the mitochondrial membrane permeability. Colon carcinogenesis was initiated in Wistar rats by intra-peritoneal injections of azoxymethane (AOM), once a week for 2 weeks. One week after the last injection, rats received lupulones (0.001 or 0.005%) in drinking water, and AOM-control rats received the excipient. After 7 months of treatment, the colon of rats receiving 0.001 and 0.005% lupulones showed, respectively, a 30 and a 50% reduction (P < 0.05) of the number of preneoplastic lesions (aberrant crypt foci). In addition, we observed a drastic reduction (70-80%) of the total number of tumors in the colon of rats treated with lupulones when compared with the AOM control group. Lupulones induced apoptosis in SW620 colon-derived metastatic cells by activating both Fas and TRAIL death receptor signaling pathways, and antagonize at a low dose (4 mg/kg/day) colon cancer development. These observations suggest the use of lupulones for colon cancer chemoprevention trials.
ChemInform Abstract: SYNTHESIS OF MESO‐SUBSTITUTED TRICARBOCYANINE DYES WITH AN O‐PHENYLENE BRIDGE IN THE CHROMOPHORE (1984)

Abstract Durch Reaktion des Komplexes aus DMF und POCl 3 mit 2‐Ethoxy‐ (II) bzw. 2‐Phenylinden (VIII), beide erhalten aus dem Indanon (I), werden die Glutaconaldehydderivate (III) bzw. (IX) mit o‐Phenylenbrücke in der konjugierten Kette erhalten.
Wnt/β-catenin signaling is required for CNS, but not non-CNS, angiogenesis (2009)

Despite the importance of CNS blood vessels, the molecular mechanisms that regulate CNS angiogenesis and blood-brain barrier (BBB) formation are largely unknown. Here we analyze the role of Wnt/beta-catenin signaling in regulating the formation of CNS blood vessels. First, through the analysis of TOP-Gal Wnt reporter mice, we identify that canonical Wnt/beta-catenin signaling is specifically activated in CNS, but not non-CNS, blood vessels during development. This activation correlates with the expression of different Wnt ligands by neural progenitor cells in distinct locations throughout the CNS, including Wnt7a and Wnt7b in ventral regions and Wnt1, Wnt3, Wnt3a, and Wnt4 in dorsal regions. Blockade of Wnt/beta-catenin signaling in vivo specifically disrupts CNS, but not non-CNS, angiogenesis. These defects include reduction in vessel number, loss of capillary beds, and the formation of hemorrhagic vascular malformations that remain adherent to the meninges. Furthermore, we demonstrate that Wnt/beta-catenin signaling regulates the expression of the BBB-specific glucose transporter glut-1. Taken together these experiments reveal an essential role for Wnt/beta-catenin signaling in driving CNS-specific angiogenesis and provide molecular evidence that angiogenesis and BBB formation are in part linked.
Interactions Between Mastoparan B and the Membrane Studied by1H NMR Spectroscopy (2001)

Mastoparan B (MP-B) is an antimicrobial cationic tetradecapeptide amide isolated from the venom of the hornet Vespa basalis. NMR spectroscopy was used to study the membrane associated structures of MP-B in various model membrane systems such as 120 mM DPC micelles, 200 mM SDS micelles, and 3%(w/v) DMPC/DHPC (1:2) bicelles. In all systems, MP-B has an amphiphilic alpha-helical structure from Lys2 to Leu14. NOESY experiments performed on MP-B in nondeuterated SDS micelles show that protons in the indole ring of Trp9 are in close contact with methylene protons of SDS micelles. T1 relaxation data and NOE data revealed that the bound form of MP-B may be dominant in SDS micelles. The interactions between MP-B and zwitterionic DPC micelles were much weaker than those between MP-B and anionic SDS micelles. By substitution of Trp9 with Ala9, the pore-forming activity of MP-B was decreased dramatically. All of these results imply that strong electrostatic interactions between the positively charged Lys residues in MP-B and the anionic phospholipid head groups must be the primary factor for MP-B binding to the cell membrane. Then, insertion of the indole ring of Trp9 into the membrane, as well as the amphiphilic alpha-helical structures of MP-B may allow MP-B to span the lipid bilayer through the C-terminal portion. These structural features are crucial for the potent antibiotic activities of MP-B.
A More Sensitive Plate Assay for Detection of Protease Production by Pseudomonas aeruginosa (1979)

A plate assay to measure protease production by Pseudomonas aeruginosa is described. This assay is more sensitive and rapid than established methods.
Expanded‐Bed Adsorption Chromatography (2005)

Expanded-bed adsorption (EBA) chromatography is a convenient and effective technique for the capture of proteins directly from unclarified crude sample. In EBA chromatography, the settled bed is first expanded by upward flow of equilibration buffer. The crude feed, a mixture of soluble proteins, contaminants, cells, and cell debris, is then passed upward through the expanded bed. Target proteins are captured on the adsorbent, while particulates and contaminants pass through. A change to elution buffer while maintaining upward flow results in desorption of the target protein in expanded-bed mode. Alternatively, if the flow is reversed, the adsorbed particles will quickly settle and the proteins can be desorbed by an elution buffer. The mode used for elution (expanded-bed versus settled-bed) depends on the characteristics of the feed. After elution, the adsorbent is cleaned with a predefined cleaning-in-place (CIP) solution, with cleaning followed by either column regeneration (for further use) or storage.
Ketamine for pain management (2018)

Supplemental Digital Content is Available in the Text.
Elastin-Based Side-Chain Polymers:  Improved Synthesis via RAFT and Stimulus Responsive Behavior (2007)

Elastin-based side-chain polymers (EBPs) were prepared by the polymerization of a methacrylate derivative of the pentapeptide valine−proline−glycine−valine−glycine (VPGVG) using reversible addition−fragmentation chain transfer (RAFT) polymerization. The polymerizations proceeded in a controlled manner, yielding polymers with a narrow molecular weight distribution (polydispersity indices 1.03−1.23) and molecular weights in good agreement with those predicted from the initial monomer:initiator ratio for the conversion obtained. The dithioester end groups of the resulting polymers were removed by reaction with azo initiator-derived radicals. The lower critical solution temperature (LCST) behavior of the series of EBPs so obtained was investigated in solutions of varying pH (1.5−5.1) and polymer concentration (0.11−0.97 mg/mL) and for polymers of different degrees of polymerization (29−88 repeating units). These EBPs behaved similarly to linear polypeptides, known as elastin-like peptides (ELPs); the transition temperature decreased with increasing polymer concentration and molecular weight. Unlike ELPs, but in common with previously reported EBPs, a strong dependence of transition temperature on pH was observed due to the presence of the carboxylic acid from the C-terminal residue in the peptide side chains. Significant differences between the EBPs described here and those reported earlier were found, however, regarding the transition temperature at a given pH and its variation with molecular weight. These variations are attributed to differences in architecture between the polymers described here (higher molecular weight homopolymers) and those reported earlier (A−B−A triblock copolymers with short EBP A blocks and a PEG B block).
The multiphoton ionization spectrum of t r a n s-1,3-butadiene (1976)

The multiphoton ionization spectrum of trans-1,3-butadiene has been measured from dye laser wavelengths of 365 to 468 nm using an intensity-corrected system. In the four-photon ionization region to lower energy than 405 nm, many three-photon resonances with Rydberg states are seen and a new series with a quantum defect of 0.04 is identified. The symmetries of the observed Rydberg series are discussed. Above 405 nm in energy, a resonance occurs with the ? state seen in one-photon absorption spectra, only the structure in the multiphoton ionization spectrum is characteristic of an allowed two-photon resonance. From the vibronic structure of this state, it is argued that it has symmetry 1Bg. In the region covered by this study (42 700 to 54 800 cm−1 in two-photon energy) no state was found to which a 1Ag symmetry designation could be applied.
Rosiglitazone and Cognitive Stability in Older Individuals With Type 2 Diabetes and Mild Cognitive Impairment (2010)

Rosiglitazone may protect against cognitive decline in older individuals with type 2 diabetes and MCI.
Room-Temperature Single-Nucleotide Polymorphism and Multiallele DNA Detection Using Fluorescent Nanocrystals and Microarrays (2003)

We report two cDNA microarray-based applications of DNA-nanocrystal conjugates, single-nucleotide polymorphism (SNP) and multiallele detections, using a commercial scanner and two sets of nanocrystals with orthogonal emissions. We focus on SNP mutation detection in the human p53 tumor suppressor gene, which has been found to be mutated in more than 50% of the known human cancers. DNA-nanocrystal conjugates are able to detect both SNP and single-base deletion at room temperature within minutes, with true-to-false signal ratios above 10. We also demonstrate microarray-based multiallele detection, using hybridization of multicolor nanocrystals conjugated to two sequences specific for the hepatitis B and hepatitis C virus, two common viral pathogens that inflict more than 10% of the population in the developing countries worldwide. The simultaneous detection of multiple genetic markers with microarrays and DNA-nanocrystal conjugates has no precedent and suggests the possibility of detecting an even greater number of bacterial or viral pathogens simultaneously.