gebhart/patrepeval huggingface dataset:
Characterization of the active site cysteine residues of the thioredoxin-like domains of protein disulfide isomerase (1995)

The dithiol/disulfide active sites of each of the two isolated thioredoxin-like domains of protein disulfide isomerase (PDI) expressed in Escherichia coli have been characterized in order to understand their catalytic mechanisms and their functions in PDI. In each of the folded domains, as in other proteins of the thioredoxin family, only one of the cysteine residues of the active site sequence -Cys-Gly-His-Cys- is accessible, and its thiol group is highly reactive and has a low pKa value. The kinetics and equilibria have been measured of the reactions between the active site cysteine residues and glutathione, the predominant thiol/disulfide reagent of the endoplasmic reticulum. A disulfide bond can be formed very rapidly between the pair of cysteine residues of each domain, but each disulfide bond is very unstable and reacts rapidly with reduced glutathione. The very low stabilities of these disulfide bonds, which destabilize the protein structures, account for the efficiency with which PDI and each of the isolated domains can introduce disulfide bonds into proteins. These kinetics and equilibrium data go far in helping to understand the catalytic mechanism of PDI and its individual domains.
Effects of Induced Hypothermia on Subcortical Evoked Potentials in the Cat (1958)

The effects of induced hypothermia in the unanesthetized immobilized cat on somatic afferent evoked potentials from the posteroventral lateral nucleus of the thalamus, periaqueductal midbrain reticular formation and dorsal column of the spinal cord were studied in 28 cats. At a rectal temperature of 23°C, marked depression of the responses recorded from all loci was demonstrable. The afferent midbrain reticular formation was demonstrated to be more sensitive to hypothermia than the thalamic relay nucleus. Augmentation of the spinal cord dorsal column evoked potentials was noted between 33°C and 25°C. Conduction time measurements indicated that between 37°C and 27°C the velocity of transmission along the nerve fibers is more affected than transmission across a synapse.
Biomimetic recognition elements for sensor applications (1997)

Ethanol and other alcohols with low molecular mass, glucose and creatinine are the analytes and/or substrates which have to be most frequently determined to obtain analytical informations in a variety of different process. The extensive literature on the development of biosensors is indicative of the interest in these sensors. In addition to enzyme-coupled recognition in biosensors, chemical host-guest interactions based on synthetic hosts are currently being investigated. Such a research project has applied an optical ethanol sensor to monitor ethanol generation in a bioreactor continuously. In this chapter, some examples of the state-of-the-art and recent results of these research projects are presented. Difficulties encountered in coupling a transducer to the synthetic host-guest recognition process, and in two-phase systems are described.
A Broadly Applicable Method for the Efficient Synthesis of α-O-Linked Glycopeptides and Clustered Sialic Acid Residues (1999)

The total syntheses of complex sialylated cell-surface antigens have been accomplished. The target systems include 2,3-STF, STn, 2,6-STF, and glycophorin antigens. In addition, an α-O-linked serine glycoside of an entire Lewis blood group (Y) antigen has been assembled.
Isolation of a Plant Glycoprotein Involved with Control of Intercellular Recognition (1981)

A recognition molecule was isolated from stigmas of S-allele genotype S(2)S(2) of Brassica oleracea var. capitata L. After Sephadex chromatography, it eluted as a single symmetrical peak during diethylaminoethane-cellulose chromatography. A high degree of purity was affirmed by: sedimentation as a single peak during ultracentrifugation through 5 to 20% sucrose gradients; elution as a single peak from Sephadex G-100; visualization as a single band which stains with Coomassie blue and periodic acid Schiff reagent after electrophoresis on polyacrylamide gels. Other criteria supporting the conclusion that it is a glycoprotein are: (a) the highly purified preparation is anthrone-positive and has a Lowry protein to anthrone-positive carbohydrate ratio of 1.3; (b) the preparation contains arabinose, galactose, glucose, and mannose, although it is not precipitated by concanavalin A; (c) the immunological properties of the molecule are lost following protease treatment, and it has a molecular weight of 90,000 by Sephadex gel-filtration analysis and 54,500 by velocity sedimentation analysis.In vitro pretreatment of S(2)S(2) pollen with the post-diethylaminoethane-purified S(2) glycoprotein prevented the S(2)S(2) pollen from germinating on three classes of compatible stigmas: (a) mature stigmas of genotypes S(3)S(3) and S(8)S(8), which are non-self genotypes; (b) immature stigmas of genotype S(2)S(2), where incompatibility is not expressed; and (c) mature stigmas with a recessive S(2) allele. Pretreatment of S(3)S(3) and S(8)S(8) pollen with the S(2) glycoprotein did not interfere with their germination.
Selective Catalytic Dimerization of Neohexene by [Cp*Ti(NPtBu3)Me][B(C6F5)4] (2008)

The known titanium alkyl cation [Cp*Ti(NPtBu3)Me][B(C6F5)4], supported by a bulky phosphinimide donor, was found to react with 3 equiv of 3,3-dimethyl-1-butene (neohexene) to generate another alkyl cation in which the alkyl group is derived from two dimerized equivalents of the substrate olefin. This species, 1, was characterized in detail by spectroscopic methods and via X-ray crystallographic determinations of two of its derivatives, the THF adduct (2) and the neutral chloride derivative 3 formed upon addition of Cl− to 1. Detailed mechanistic experiments suggest 1 is formed via insertion of neohexene into the Ti−Me bond of [Cp*Ti(NPtBu3)Me][B(C6F5)4] to give a detectable intermediate (4), which was characterized spectroscopically. Cation 4 reacts in a σ-bond metathesis reaction with the olefinic C−H bond trans to the tert-butyl group of another equivalent of neohexene to form an undetected cationic vinyl intermediate, which rapidly inserts a third equivalent of neohexene to generate 1. Deuterium labeling studies are consistent with this mechanistic picture. Compound 1 is the resting state of a catalytic cycle for dimerization of neohexene; under catalytic conditions (95 °C, [neohexene] = 1.1 M, 1.2−2.1 mol% 1), clean conversion of neohexene to (E)-2,2,5,6,6-pentamethylhept-3-ene was observed, with total turnovers of 44—78.
Peptide Binding to Class I Molecules of the Major Histocompatibility Complex on the Surface of Living Target Cells (1992)

Molecules encoded by the class I major histocompatibility genes bind short (nonameric) peptides produced by intracellular proteolysis of antigens. These complexes formed intracellularly are then expressed on membranes of target cells and recognized by the antigen receptor of cytolytic T cells. No binding of externally added peptides could so far be monitored directly on the antigen presenting cells, although cytotoxicity experiments and indirect binding assays provided evidence for its existence. Here we report experiments where specific binding to class I molecules, of externally added peptides, has been monitored on living cells. N-terminal biotin-labelled Kd-restricted peptides (residues 147-155, residues 147-158, and an analogue lacking the arginine at position 156, derived from the sequence of the influenza A virus nucleoprotein) were incubated with murine H-2Kd mastocytoma cells (line P815) at 4 degrees C. The binding on surface of live, intact cells was then demonstrated fluorometrically via the interaction of a streptavidin-phycoerythrin conjugate with the biotin-labelled peptides. Thus, this binding does not involve processing, and its specificity in terms of peptide structure was established by competition with the respective unmodified peptides. The specificity of binding to class I molecules was demonstrated by blocking experiments using monoclonal antibodies specific for H-2Kd. Finally, a correlation was observed between the results of peptide binding measurements and those of cytotoxicity assays.
Role Discovery in Networks (2014)

Roles represent node-level connectivity patterns such as star-center, star-edge nodes, near-cliques or nodes that act as bridges to different regions of the graph. Intuitively, two nodes belong to the same role if they are structurally similar. Roles have been mainly of interest to sociologists, but more recently, roles have become increasingly useful in other domains. Traditionally, the notion of roles were defined based on graph equivalences such as structural, regular, and stochastic equivalences. We briefly revisit these early notions and instead propose a more general formulation of roles based on the similarity of a feature representation (in contrast to the graph representation). This leads us to propose a taxonomy of three general classes of techniques for discovering roles that includes (i) graph-based roles, (ii) feature-based roles, and (iii) hybrid roles. We also propose a flexible framework for discovering roles using the notion of similarity on a feature-based representation. The framework consists of two fundamental components: (a) role feature construction and (b) role assignment using the learned feature representation. We discuss the different possibilities for discovering feature-based roles and the tradeoffs of the many techniques for computing them. Finally, we discuss potential applications and future directions and challenges.
Studies on the Pyrimidine Derivatives. XXVII. A New Method for Synthesis of Diethyl Ethoxycarbonylphosphite from Tris (ethoxythiocarbonyl) Phosphorotrithioite, and on the Reactions of these Organo-phosphorus Compounds with Thiamine Sodium Salt. (1964)

On the reaction of potassium O-ethyl thiocarbonate (I) or potassium O-ethyl dithiocarbonate (IV) with phosphorus trichloride, tris (ethoxycarbonyl) phosphorotrithioite (IIa) or tris (ethoxythiocarbonyl) phosphorotrithioite (V) were synthesized, respectively. From the treatment of IIa or V with ethyl chloroformate, the same product, diethyl ethoxy-carbonylphosphite (IIIa), accompanied by carbonyl sulfide and ethyl chloride from IIa, and carbon disulfide and ethyl chloride from V, were given in high yield. When tris (alkoxycarbonyl) phosphorotrithioite (II) and thiamine sodium salt (VII) were reacted together, O, S-bis (alkoxycarbonyl) thiamine (IX) was produced. On the other hand, from the reaction of dialkyl ethoxycarbonylphosphite with VII, O, S-bis (ethoxycarbonyl)-thiamine (IXa) was also obtained, but in this cases S-alkylthiamines were main products.
Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA (2014)

RNA-guided endonucleases (RGENs) derived from the CRISPR/Cas system represent an efficient tool for genome editing. RGENs consist of two components: Cas9 protein and guide RNA. Plasmid-mediated delivery of these components into cells can result in uncontrolled integration of the plasmid sequence into the host genome, and unwanted immune responses and potential safety problems that can be caused by the bacterial sequences. Furthermore, this delivery method requires transfection tools. Here we show that simple treatment with cell-penetrating peptide (CPP)-conjugated recombinant Cas9 protein and CPP-complexed guide RNAs leads to endogenous gene disruptions in human cell lines. The Cas9 protein was conjugated to CPP via a thioether bond, whereas the guide RNA was complexed with CPP, forming condensed, positively charged nanoparticles. Simultaneous and sequential treatment of human cells, including embryonic stem cells, dermal fibroblasts, HEK293T cells, HeLa cells, and embryonic carcinoma cells, with the modified Cas9 and guide RNA, leads to efficient gene disruptions with reduced off-target mutations relative to plasmid transfections, resulting in the generation of clones containing RGEN-induced mutations. Our CPP-mediated RGEN delivery process provides a plasmid-free and additional transfection reagent-free method to use this tool with reduced off-target effects. We envision that our method will facilitate RGEN-directed genome editing.
Procaryotic Expression of Single-Chain Variable-Fragment (scFv) Antibodies: Secretion in L-Form Cells of Proteus mirabilis Leads to Active Product and Overcomes the Limitations of Periplasmic Expression in Escherichia coli (1998)

Recently it has been demonstrated that L-form cells of Proteus mirabilis (L VI), which lack a periplasmic compartment, can be efficiently used in the production and secretion of heterologous proteins. In search of novel expression systems for recombinant antibodies, we compared levels of single-chain variable-fragment (scFv) production in Escherichia coli JM109 and P. mirabilis L VI, which express four distinct scFvs of potential clinical interest that show differences in levels of expression and in their tendencies to form aggregates upon periplasmic expression. Production of all analyzed scFvs in E. coli was limited by the severe toxic effect of the heterologous product as indicated by inhibition of culture growth and the formation of insoluble aggregates in the periplasmic space, limiting the yield of active product. In contrast, the L-form cells exhibited nearly unlimited growth under the tested production conditions for all scFvs examined. Moreover, expression experiments with P. mirabilis L VI led to scFv concentrations in the range of 40 to 200 mg per liter of culture medium (corresponding to volume yields 33- to 160-fold higher than those with E. coli JM109), depending on the expressed antibody. In a translocation inhibition experiment the secretion of the scFv constructs was shown to be an active transport coupled to the signal cleavage. We suppose that this direct release of the newly synthesized product into a large volume of the growth medium favors folding into the native active structure. The limited aggregation of scFv observed in the P. mirabilis L VI supernatant (occurring in a first-order-kinetics manner) was found to be due to intrinsic features of the scFv and not related to the expression process of the host cells. The P. mirabilis L VI supernatant was found to be advantageous for scFv purification. A two-step chromatography procedure led to homogeneous scFv with high antigen binding activity as revealed from binding experiments with eukaryotic cells.
Parameters Underlying Distinct T Cell-Dependent Polysaccharide-Specific IgG Responses to an Intact Gram-Positive Bacterium versus a Soluble Conjugate Vaccine (2009)

IgG anti-polysaccharide (PS) responses to both intact Streptococcus pneumoniae (Pn) and PS conjugate vaccines are dependent on CD4(+) T cells, B7-dependent costimulation, and CD40-CD40-ligand interactions. Nevertheless, the former response, in contrast to the latter, is mediated by an ICOS-independent, apoptosis-prone, extrafollicular pathway that fails to generate PS-specific memory. We show that pre-existing PS-specific Igs, the bacterial surface or particulation, selective recruitment of B cell subsets, or activation and recruitment of Pn protein-specific CD4(+) T cells do not account for the failure of Pn to generate PS-specific IgG memory. Rather, the data suggest that the critical factor may be the lack of covalent attachment of PS to protein in intact Pn, highlighting the potential importance of the physicochemical relationship of PS capsule with the underlying bacterial structure for in vivo induction of PS-specific Igs.
The periodontopathogen Porphyromonas gingivalis binds iron protoporphyrin IX in the μ-oxo dimeric form: an oxidative buffer and possible pathogenic mechanism (1998)

Mössbauer spectroscopy was used to re-evaluate iron protoporphyrin IX, FePPIX, binding and the chemical nature of the black iron porphyrin pigment of Porphyromonas gingivalis. We demonstrate that FePPIX is bound to the cell in the mu-oxo dimeric form, [Fe(III)PPIX]2O, and that the iron porphyrin pigment is also composed of this material. P. gingivalis also assimilated monomeric Fe(II)- and Fe(III)PPIX into mu-oxo dimers in vitro. Scatchard analysis revealed a greater binding maximum of cells for mu-oxo dimers than for monomeric Fe(III)-or Fe(II)PPIX, although the relative affinity constant for the dimers was lower. Formation of [Fe(III)PPIX]2O via reactions of Fe(II)PPIX with oxygen, and its toxic derivatives, would serve as an oxidative buffer and permit P. gingivalis and other black-pigmenting anaerobes to engender and maintain a local anaerobic environment. Tying up of free oxygen species with iron protoporphyrin IX would also reduce and limit Fe(II)PPIX-mediated oxygen-radical cell damage. More importantly, formation of a cell-surface mu-oxo dimer layer may function as a protective barrier against assault by reactive oxidants generated by neutrophils. Selective interference with these mechanisms would offer the possibility of attenuating the pathogenicity of P. gingivalis and other iron protoporphyrin IX-binding pathogens whose virulence is regulated by this reactive molecule.
Carbohydrate‐based poly(ester‐urethane)s: A comparative study regarding cyclic alditols extenders and polymerization procedures (2009)

Abstract A set of segmented poly(ester‐urethane)s were prepared from diisocyanates HDI or MDI and using 1,4‐butanediol and D ‐glucose‐derived cyclic diols (1,4 : 3,6‐dianhydro‐ D ‐glucitol (isosorbide) or 2,4;3,5‐di‐ O ‐methylidene‐ D ‐glucitol (gludioxol) or mixtures of them) as extenders. Hydroxyl end‐capped polycaprolactone with a molecular weight of 3000 g·mol −1 was used as soft segment. Two polymerization methods, in solution and in bulk, were applied for the synthesis of these poly(ester‐urethane)s. The influence of the preparation procedure and composition in cyclic extender on synthesis results, structure, and properties of the novel poly(ester‐urethane)s was comparatively evaluated and discussed. The effect of replacement of 1,4‐butanediol by isosorbide or gludioxol on hydrodegradability was also assessed; the hydrolysis rate increased noticeably with the presence of glucitol derived units, although degradation of the polymers took place essentially by hydrolysis of the polyester soft segment. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Erythropoietin in Cancer Patients (2008)

Therapy with erythropoiesis-stimulating agents (ESAs) is associated with well-documented benefits to anemic cancer patients undergoing chemotherapy, most importantly a reduction in the likelihood of needing red cell transfusions. One challenge in supportive cancer care is a relative resistance to ESAs, requiring high doses with a significant rate of nonresponse. Recent advances in our understanding of iron metabolism in patients with chronic illness and the results of clinical trials indicate that parenteral iron improves ESA response in this setting. Another issue is the safety of ESA treatment in cancer patients. There is an increased risk of venous thrombosis that must be considered in clinical decision making. There are also recent data raising concerns that ESAs may enhance tumor progression or decrease patient survival. Although the preponderance of the data suggests that ESAs do not alter survival when used to treat chemotherapy-induced anemia, large well-controlled trials addressing this issue are needed.
Targeted and high relaxivity contrast agents. (2001)

The peculiar magnetic properties of Gd(III) ion make it ideal for use as contrast agent (CA) for Magnetic Resonance Imaging (MRI).However, due to its high toxicity, gadolinium ions must be administered in the form of thermodynamically and kinetically stable complexes.The relatively high doses required and the low efficiency of the commercially available CA currently in use, have stimulated the search for new classes of such diagnostic compounds.In the first part of this work a new stable, high relaxivity, di-aqua gadolinium complex has been synthesized and its properties studied in detail.The presence of two water molecules in the coordination sphere of the complex increases its efficiency as a contrast agent.So far the failure to develop practicable dihydrated systems has arisen mainly from the insufficient kinetic and thermodynamic stability associated with such complexes.In addition, each of the di-aqua complexes published in the literature have exhibited a high affinity towards the binding, either of endogenous anions (e. g. phosphate or carbonate) or of proteins, such as Human Serum Albumin (HSA).This binding contributes strongly to the decrease of the relaxivity of the complexes.In contrast, the anionic di-aqua complex herein described should be suitable as the basis of an MRI agent, because it possesses sufficient stability, with respect to acid or cation mediated dissociation pathways, has a fast rate of water exchange (30ns at 298K), a high relaxivity (12.3 mM's-1 at 20 MHz and 298K) and minimizes competing anion/protein binding.In the second part of this work new targeted contrast agents have been prepared and studied.In order to target specifically cancerous tissues, gadolinium chelates have been coupled to folic acid, which is overexpressed in certain types of cancerous cells.A tetra a-substituted DOTA derivative complex, has been chosen which for its optimal intrinsic relaxometric properties (i.e. faster water exchange, enhanced relaxivity).The affinity of its folate derivative for folate binding protein (FBP) has been investigated and compared to that of a nonspecific protein (i.e HSA).The 83% enhancement in relaxivity in the presence of FBP clearly demonstrated that this receptor protein FBP is capable of recognizing this complex selectively.All the people who have been working with me in the Wolfson Laboratory (CG27) in Durham.In particular Mark Lowe, for his advises and helps for the relaxivity measurements and for synthesizing some of the compounds I used and James Bruce for the luminescence studies.Thanks to
A Novel Phosphopantetheine:Protein Transferase Activating Yeast Mitochondrial Acyl Carrier Protein (1998)

In Saccharomyces cerevisiae, the low molecular weight acyl carrier protein (ACP) of mitochondrial type II fatty acid synthase (FAS) and the cytoplasmic type I FAS multienzyme contain 4'-phosphopantetheine as a prosthetic group. Sequence alignment studies with the recently isolated phosphopantetheine:protein transferase (PPTase), Ppt1p, from Brevibacterium ammoniagenes revealed the yeast open reading frame, YPL148C, as a potential PPTase gene (25% identical and 43% conserved amino acids). In accordance with this similarity, pantetheinylation of mitochondrial ACP was lost upon disruption of YPL148C. In contrast, biosynthesis of cytoplasmic holo-FAS remained unaffected by this mutation. According to these characteristics, the newly identified gene was designated as PPT2. Similar to ACP null mutants, cellular lipoic acid synthesis and, hence, respiration were abolished in PPT2 deletants. ACP pantetheinylation, lipoic acid synthesis, and respiratory competence were restored upon transformation of PPT2 mutants with cloned PPT2 DNA. In vitro, holo-ACP synthesis was achieved by incubating apo-ACP with coenzyme A in the presence of purified Ppt2p. The homologous yeast enzyme could be replaced, in this assay, by the ACP synthase (EC 2.7.8.7) of Escherichia coli but not by the type I FAS-specific PPTase of B. ammoniagenes, Ppt1p. These results conform with the inability of Ppt2p to activate the cytoplasmic type I FAS complex of yeast.