gebhart/patrepeval huggingface dataset:
Two novel protein-tyrosine kinases, each with a second phosphotransferase-related catalytic domain, define a new class of protein kinase. (1991)

The protein-tyrosine kinases (PTKs) are a burgeoning family of proteins, each of which bears a conserved domain of 250 to 300 amino acids capable of phosphorylating substrate proteins on tyrosine residues. We recently exploited the existence of two highly conserved sequence elements within the catalytic domain to generate PTK-specific degenerate oligonucleotide primers (A. F. Wilks, Proc. Natl. Acad. Sci. USA 86:1603-1607, 1989). By application of the polymerase chain reaction, portions of the catalytic domains of several novel PTKs were amplified. We describe here the primary sequence of one of these new PTKs, JAK1 (from Janus kinase), a member of a new class of PTK characterized by the presence of a second phosphotransferase-related domain immediately N terminal to the PTK domain. The second phosphotransferase domain bears all the hallmarks of a protein kinase, although its structure differs significantly from that of the PTK and threonine/serine kinase family members. A second member of this family (JAK2) has been partially characterized and exhibits a similar array of kinase-related domains. JAK1 is a large, widely expressed membrane-associated phosphoprotein of approximately 130,000 Da. The PTK activity of JAK1 has been located in the C-terminal PTK-like domain. The role of the second kinaselike domain is unknown.
Insecticidal crystal proteins of Bacillus thuringiensis (1989)

A classification for crystal protein genes of Bacillus thuringiensis is presented. Criteria used are the insecticidal spectra and the amino acid sequences of the encoded proteins. Fourteen genes are distinguished, encoding proteins active against either Lepidoptera (cryI), Lepidoptera and Diptera (cryII), Coleoptera (cryIII), or Diptera (cryIV). One gene, cytA, encodes a general cytolytic protein and shows no structural similarities with the other genes. Toxicity studies with single purified proteins demonstrated that every described crystal protein is characterized by a highly specific, and sometimes very restricted, insect host spectrum. Comparison of the deduced amino acid sequences reveals sequence elements which are conserved for Cry proteins. The expression of crystal protein genes is affected by a number of factors. Recently, two distinct sigma subunits regulating transcription during different stages of sporulation have been identified, as well as a protein regulating the expression of a crystal protein at a posttranslational level. Studies on the biochemical mechanisms of toxicity suggest that B. thuringiensis crystal proteins induce the formation of pores in membranes of susceptible cells. In vitro binding studies with radiolabeled toxins demonstrated a strong correlation between the specificity of B. thuringiensis toxins and the interaction with specific binding sites on the insect midgut epithelium. The expression of B. thuringiensis crystal proteins in plant-associated microorganisms and in transgenic plants has been reported. These approaches are potentially powerful strategies for the protection of agriculturally important crops against insect damage.
Prediction of the tertiary structure and substrate binding site of caspase‐8 (1997)

The caspases represent a family of sulfhydryl proteases that play important regulatory roles in the cell. The tertiary structure of the protease domain of caspase-8, also called FLICE, has been predicted by a segment match modeling procedure. First, the atomic coordinates of the catalytic domain of caspase-3, also called CPP32, a member of the family that is closely related to caspase-8, were determined based upon the crystal structure of human caspase-1 (interleukin converting enzyme). Then, the caspase-3 structure was used as a template for modeling the protease domain of caspase-8. The resulting structure shows the expected level of similarity with the conformations of caspases-1 and -3 for which crystal structures have been determined. Moreover, the subsite contacts between caspase-8 and the covalently linked inhibitor, Ac-DEVD-aldehyde, are only slightly different from those seen in the caspase-3 enzyme/inhibitor complex. The model of caspase-8 can serve as a reference for subsite analysis relative to design of enzyme inhibitors that may find therapeutic application.
Quantitative Observation of Backbone Disorder in Native Elastin (2004)

Elastin is a key protein in soft tissue function and pathology. Establishing a structural basis for understanding its reversible elasticity has proven to be difficult. Complementary to structure is the important aspect of flexibility and disorder in elastin. We have used solid-state NMR methods to examine polypeptide and hydrate ordering in both elastic (hydrated) and brittle (dry) elastin fibers and conclude (i) that tightly bound waters are absent in both dry and hydrated elastin and (ii) that the backbone in the hydrated protein is highly disordered with large amplitude motions. The hydrate was studied by (2)H and (17)O NMR, and the polypeptide by (13)C and (2)H NMR. Using a two-dimensional (13)C MAS method, an upper limit of S < 0.1 was determined for the backbone carbonyl group order parameter in hydrated elastin. For comparison, S approximately approximately 0.9 in most proteins. The former result is substantiated by two additional observations: the absence of the characteristic (2)H spectrum for stationary amides and "solution-like" (13)C magic angle spinning spectra at 75 degrees C, at which the material retains elasticity. Comparison of the observed shifts with accepted values for alpha-helices, beta-sheets, or random coils indicates a random coil structure at all carbons. These conclusions are discussed in the context of known thermodynamic properties of elastin and, more generally, protein folding. Because coacervation is an entropy-driven process, it is enhanced by the observed backbone disorder, which, we suggest, is the result of high proline content. This view is supported by recent studies of recombinant elastin polypeptides with systematic proline substitutions.
Transient “rest” induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells (2020)

SUMMARY T cell exhaustion limits immune responses against cancer and is a major cause of resistance to CAR-T cell therapeutics. Using a model wherein tonic CAR signaling induces hallmark features of exhaustion, we employed a drug-regulatable CAR to test the impact of transient cessation of receptor signaling (i.e. “rest”) on the development and maintenance of exhaustion. Induction of rest in exhausting or already-exhausted CAR-T cells resulted in acquisition of a memory-like phenotype, improved anti-tumor functionality, and wholescale transcriptional and epigenetic reprogramming. Similar results were achieved with the Src kinase inhibitor dasatinib, which reversibly suppresses CAR signaling. The degree of functional reinvigoration was proportional to the duration of rest and was associated with expression of transcription factors TCF1 and LEF1. This work demonstrates that transient cessation of CAR-T cell signaling can enhance anti-tumor potency by preventing or reversing exhaustion and challenges the paradigm that exhaustion is an epigenetically fixed state.
Dehydration of Alcohols, Diols, and Related Compounds in Dimethyl Sulfoxide1 (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDehydration of Alcohols, Diols, and Related Compounds in Dimethyl Sulfoxide1Vincent J. Traynelis, William L. Hergenrother, Harry T. Hanson, and John A. ValicentiCite this: J. Org. Chem. 1964, 29, 1, 123–129Publication Date (Print):January 1, 1964Publication History Published online1 May 2002Published inissue 1 January 1964https://pubs.acs.org/doi/10.1021/jo01024a028https://doi.org/10.1021/jo01024a028research-articleACS PublicationsRequest reuse permissionsArticle Views1582Altmetric-Citations90LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Specific, irreversible inactivation of the epidermal growth factor receptor and erbB2, by a new class of tyrosine kinase inhibitor (1998)

A class of high-affinity inhibitors is disclosed that selectively target and irreversibly inactivate the epidermal growth factor receptor tyrosine kinase through specific, covalent modification of a cysteine residue present in the ATP binding pocket. A series of experiments employing MS, molecular modeling, site-directed mutagenesis, and 14C-labeling studies in viable cells unequivocally demonstrate that these compounds selectively bind to the catalytic domain of the epidermal growth factor receptor with a 1:1 stoichiometry and alkylate Cys-773. While the compounds are essentially nonreactive in solution, they are subject to rapid nucleophilic attack by this particular amino acid when bound in the ATP pocket. The molecular orientation and positioning of the acrylamide group in these inhibitors in relation to Cys-773 entirely support these results as determined from docking experiments in a homology-built molecular model of the ATP site. Evidence is also presented to indicate that the compounds interact in an analogous fashion with erbB2 but have no activity against the other receptor tyrosine kinases or intracellular tyrosine kinases that were tested in this study. Finally, a direct comparison between 6-acrylamido-4-anilinoquinazoline and an equally potent but reversible analog shows that the irreversible inhibitor has far superior in vivo antitumor activity in a human epidermoid carcinoma xenograft model with no overt toxicity at therapeutically active doses. The activity profile for this compound is prototypical of a generation of tyrosine kinase inhibitors with great promise for therapeutic significance in the treatment of proliferative disease.
Neutralization Escape Variants of Human Immunodeficiency Virus Type 1 Are Transmitted from Mother to Infant (2005)

Maternal passive immunity typically plays a critical role in protecting infants from new infections; however, the specific contribution of neutralizing antibodies in limiting mother-to-child transmission of human immunodeficiency virus type 1 is unclear. By examining cloned envelope variants from 12 transmission pairs, we found that vertically transmitted variants were more resistant to neutralization by maternal plasma than were maternal viral variants near the time of transmission. The vertically transmitted envelope variants were poorly neutralized by monoclonal antibodies b12 [corrected] 2G12, 2F5, and 4E10 individually or in combination. Despite the fact that the infant viruses were among the most neutralization resistant in the mother, they had relatively few glycosylation sites. Moreover, the transmitted variants elicited de novo neutralizing antibodies in the infants, indicating that they were not inherently difficult to neutralize. The neutralization resistance of vertically transmitted viruses is in contrast to the relative neutralization sensitivity of viruses sexually transmitted within discordant couples, suggesting that the antigenic properties of viruses that are favored for transmission may differ depending upon mode of transmission.
A new concept for macromolecular therapeutics in cancer chemotherapy: mechanism of tumoritropic accumulation of proteins and the antitumor agent smancs. (1986)

We previously found that a polymer conjugated to the anticancer protein neocarzinostatin, named smancs, accumulated more in tumor tissues than did neocarzinostatin. To determine the general mechanism of this tumoritropic accumulation of smancs and other proteins, we used radioactive (51Cr-labeled) proteins of various molecular sizes (Mr 12,000 to 160,000) and other properties. In addition, we used dye-complexed serum albumin to visualize the accumulation in tumors of tumor-bearing mice. Many proteins progressively accumulated in the tumor tissues of these mice, and a ratio of the protein concentration in the tumor to that in the blood of 5 was obtained within 19 to 72 h. A large protein like immunoglobulin G required a longer time to reach this value of 5. The protein concentration ratio in the tumor to that in the blood of neither 1 nor 5 was achieved with neocarzinostatin, a representative of a small protein (Mr 12,000) in all time. We speculate that the tumoritropic accumulation of these proteins resulted because of the hypervasculature, an enhanced permeability to even macromolecules, and little recovery through either blood vessels or lymphatic vessels. This accumulation of macromolecules in the tumor was also found after i.v. injection of an albumin-dye complex (Mr 69,000), as well as after injection into normal and tumor tissues. The complex was retained only by tumor tissue for prolonged periods. There was little lymphatic recovery of macromolecules from tumor tissue. The present finding is of potential value in macromolecular tumor therapeutics and diagnosis.
A simple and efficient procedure for generating stable expression libraries by cDNA cloning in a retroviral vector. (1994)

cDNA expression cloning is a powerful method for the rescue and identification of genes that are able to confer a readily identifiable phenotype on specific cell types. Retroviral vectors provide several advantages over DNA-mediated gene transfer for the introduction of expression libraries into eukaryotic cells since they can be used to express genes in a wide range of cell types, including those that form important experimental systems such as the hemopoietic system. We describe here a straightforward and efficient method for generating expression libraries by using a murine retroviral vector. Essentially, the method involves the directional cloning of cDNA into the retroviral vector and the generation of pools of stable ecotropic virus producing cells from this DNA. The cells so derived constitute the library, and the virus they yield is used to infect appropriate target cells for subsequent functional screening. We have demonstrated the feasibility of this procedure by constructing several large retroviral libraries (10(5) to 10(6) individual clones) and then using one of these libraries to isolate cDNAs for interleukin-3 and granulocyte-macrophage colony-stimulating factor on the basis of the ability of these factors to confer autonomous growth on the factor-dependent hemopoietic cell line FDC-P1. Moreover, the frequency at which these factor-independent clones were isolated approximated the frequency at which they were represented in the original plasmid library. These results suggest that expression cloning with retroviruses is a practical and efficient procedure and should be a valuable method for the isolation of important regulatory genes.
Micro-coaxial V-/W-band filters and contiguous diplexers (2012)

A millimetre-wave diplexer is demonstrated using two singly terminated bandpass filters fabricated using surface micromachined rectangular-coaxial transmission lines. Modified seventh order Chebyshev bandpass filters with 0.1 dB passband ripple are designed to operate from 50 to 75 GHz and from 75 to 110 GHz. These two filters are simply combined using a common junction to form a contiguous 50–75 GHz and 75–110 GHz diplexer. The singly terminated filter values are adjusted by use of a common factor that modifies the admittance properties of the filter to facilitate their parallel combination. The two filters and their diplexer combination are fabricated and the measurements are compared favourably to the theoretical models.
Binding activity difference of anti-CD20 scFv-Fc fusion protein derived from variable domain exchange. (2006)

Two novel engineered antibody fragments binding to antigen CD20 were generated by fusing a murine IgM-type anti-CD20 single-chain Fv fragment (scFv) to the human IgG1 CH2 (i.e., Cgamma2) and CH3 (i.e., Cgamma3) domains with the human IgG1 hinge (i.e. Hgamma). Given the relationship between structure and function of protein, the 3-D structures of the two engineered antibody fragments were modeled using computer-aided homology modeling method. Furthermore, the relationship between 3-D conformation and their binding activity was evaluated theoretically. Due to the change of active pocket formed by CDRs, the HL23 (VH-Linker-VL-Hgamma-Cgamma2-Cgamma3) remained its activity because of its preserved conformation, while the binding activity of the LH23 (VL-Linker-VH-Hgamma-Cgamma2-Cgamma3) was impaired severely. Experimental studies by flow cytometry and fluorescence microscopy showed that HL23 possessed significantly superior binding activity to CD20-expressing target cells than LH23. That is to say, the order of variable regions could influence the binding activity of the fusion protein to CD20+ cell lines, which was in accordance with the theoretical results. The study highlights the potential relationship between the antibody binding activity and their 3-D conformation, which appears to be worthwhile in providing direction for future antibody design of recombinant antibody.
Stable Solution‐Processed Molecular n‐Channel Organic Field‐Effect Transistors (2012)

A new solution-processable small-molecule containing electron-poor naphthalene diimide and tetrazine moieties has been synthesized. The optimized spin-coated n-channel OFETs on glass substrate shows electron mobility value up to 0.15 cm(2) V(-1) s(-1) . Inkjet-printed OFETs are fabricated in ambient atmosphere on flexible plastic substrates, which exhibits an electron mobility value up to 0.17 cm(2) V(-1) s(-1) and also shows excellent environmental and operational stability.
Detecting Motion Regions in the Presence of a Strong Parallax from a Moving Camera by Multiview Geometric Constraints (2007)

We present a method for detecting motion regions in video sequences observed by a moving camera, in the presence of strong parallax due to static 3D structures. The proposed method classifies each image pixel into planar background, parallax or motion regions by sequentially applying 2D planar homographies, the epipolar constraint and a novel geometric constraint, called "structure consistency constraint". The structure consistency constraint, as the main contribution of this paper, is derived from the relative camera poses among three frames and implemented within the "Plane+Parallax" framework. Unlike previous planar-parallax constraints, the proposed constraint does not require the reference plane to be constant across multiple views. It directly measures the inconsistency between the projective structures from the same point under camera motion and reference plane change. The structure consistency constraint is capable of detecting moving objects followed by a moving camera in the same direction, a so called degenerate configuration where the epipolar constraint fails. We demonstrate the effectiveness and robustness of our method with experimental results on real-world video sequences.
Liposomes as in vivo carriers of adriamycin: reduced cardiac uptake and preserved antitumor activity in mice. (1982)

Abstract Neutral and negatively charged liposomes containing Adriamycin (ADM) were examined for the efficiency of drug entrapment, serum stability, in vivo tissue distribution, and tumor-inhibitory activity. Entrapment of ADM in negatively charged liposomes containing phosphatidylserine (PS) or cardiolipin (DPG) was 3- to 4-fold higher than in neutral phosphatidylcholine (PC) liposomes with or without cholesterol (Chol). In the presence of human serum, PC:Chol and PS:PC:Chol liposomes were more stable than DPG:PC:Chol liposomes, as measured by the degree of release of entrapped drug. Tissue distribution studies after i.v. injection of liposome-entrapped ADM into mice indicated that the levels of ADM were increased severalfold in the liver and the spleen. Concomitantly, the concentration of ADM in the heart was significantly diminished when the drug was delivered by PS:PC:Chol and PC:Chol liposomes but only slightly reduced when DPG:PC:Chol liposomes were used. In vitro studies with primary cell cultures of a murine lymphoma showed that the cytotoxic activity of ADM was fully preserved with the various ADM-containing liposomes used. Finally, the in vivo antitumor activity of liposome-entrapped ADM was tested on a metastatic murine lymphoma. Large multilamellar PS:PC:Chol:ADM and PC:Chol:ADM liposomes, given as a single i.v. injection, were as effective in prolonging survival as equivalent doses of free ADM. Repeated i.v. injections of small sonicated PS:PC:Chol:ADM liposomes resulted in a significantly improved survival compared to free ADM. These results indicate that the delivery of ADM by certain types of liposomes may offer an efficient means of restricting its cardiac uptake and possibly minimizing its cardiotoxicity, while preserving its antitumor therapeutic activity.
Leucine reduces the duration of insulin-induced PI 3-kinase activity in rat skeletal muscle (2004)

Leucine (Leu) is known to stimulate translation initiation of protein synthesis at mammalian target of rapamycin (mTOR) in the insulin signaling pathway. However, potential feedback from mTOR to upstream aspects of the insulin signaling pathway remains controversial. This study evaluates the impact of a physiological oral dose of Leu and/or carbohydrate (CHO) on upstream elements of the insulin signaling pathway using phosphatidylinositol 3-kinase (PI 3-kinase) activity and glucose uptake as markers for insulin sensitivity and glucose homeostasis. Rats (approximately 200 g) were fasted 12 h and administered oral doses of CHO (1.31 g glucose, 1.31 g sucrose), Leu (270 mg), or CHO plus Leu. Animals were killed at 15, 30, 60, and 90 min after treatment. Plasma and gastrocnemius muscles were collected for analyses. Treatments were designed to produce elevated blood glucose and insulin with basal levels of Leu (CHO); elevated Leu with basal levels of glucose and insulin (Leu); or a combined increase of glucose, insulin, and Leu (CHO + Leu). The CHO treatment stimulated PI 3-kinase activity and glucose uptake with no effect on the downstream translation initiation factor eIF4E. Leu alone stimulated the release of the translation initiation factor eIF4E from 4E-BP1 with no effects on PI 3-kinase activity or glucose uptake. The CHO + Leu treatment reduced the magnitude and duration of the PI 3-kinase response but maintained glucose uptake similar to the CHO treatment and eIF4E levels similar to the Leu treatment. These findings demonstrate that Leu reduces insulin-stimulated PI 3-kinase activity while increasing downstream translation initiation and with no effect on net glucose transport in skeletal muscle.