gebhart/patrepeval huggingface dataset:
Antitumour activity and specificity as a function of substitutions in the lipophilic sector of helical lactoferrin‐derived peptide (2003)

A peptide L5 (PAWRKAFRWAWRMLKKAA), derived from the N-terminal alpha-helical region of bovine lactoferrin (LFB 14-31), that is highly active against several tumour cell lines was reported earlier. In this study, a number of L5 analogues were designed in order to investigate how subsequent replacements of the aromatic amino acids in L5 with three amino acids representing different structural parameters influenced antitumour activity and tumour cell specificity relative to normal human cells. The Trp residues were substituted by Lys, Ile or Ala, while the Phe residue was substituted with Ala. The resulting peptides were investigated for their activity against prokaryotic cells, four tumour cell lines, human lung fibroblasts and human erythrocytes. Most of the peptides were highly active against both E. coli and S. aureus. The peptides were more active against the tumour cell lines than against normal eukaryotic cells but the activity against normal fibroblasts varied more among the peptides than did their antitumour activities. The results revealed that aromatic residues located opposite the cationic sector in L5 were more critical for antitumour activity than were aromatic residues located adjacent to the cationic sector. The biological responses for the peptides against tumour cell lines, fibroblasts, S. aureus (but not E. coli), were highly correlated with the amino acid descriptors used in our QSAR model. The result obtained from the QSAR study identified specific structural features that were important for lytic activity and membrane specificity. Certain structural properties in positions 3, 9 and 11 were shown to be important for antitumour activity, while additional structural properties in position 7 were found to be important with respect to tumour cell specificity. This information may offer a possibility for de novo design of an antitumour peptide with an improved therapeutic index.
Zirconium Complexes of Amine−Bis(phenolate) Ligands as Catalysts for 1-Hexene Polymerization:  Peripheral Structural Parameters Strongly Affect Reactivity (2001)

Novel amine bis(phenolate) zirconium dibenzyl complexes were synthesized in quantitative yields from a versatile family of chelating amine−bis((2-hydroxyaryl)methyl) ligand precursors, their X-ray structures solved, and their reactivity in the polymerization of 1-hexene in the presence of B(C6F5)3 studied. Several minor peripheral structural modifications were studied and found to have a major influence on the catalyst performance. Thus, a variety of reactivities, ranging from extremely high to negligible, were obtained, demonstrating a unique structure−reactivity relationship. This relationship is partially revealed from the crystal structures of the precatalysts, indicating similar [ONO] ligand cores in all structures solved. A correlation between the solid and the solution structures is obtained from 1H NMR spectra, which reveal a rigid binding of the ligand to the metal. The solid structures are therefore proposed to serve as reliable references when studying structure−reactivity relationships. The most significant structural parameter was found to be the existence of an extra donor located on a pendant arm. [ONO]-type pentacoordinate complexes lacking such an additional donor are rapidly deactivated and lead only to traces of oligomers. On the other hand, hexacoordinate complexes based on [ONNO]-type ligands, in which strong donation of a side donor to the metal is obtained through formation of a five-membered chelate, lead to extremely reactive polymerization catalysts. The nitrogen hybridization and aromatic ring substituents have a more subtle effect on reactivity. Increasing the chelate size results in either no binding of the side donor, yielding negligible reactivity, or strong binding yet moderate polymerization reactivity. Increasing the steric bulk on the donor results in weakening of the metal−donor bond, leading to a moderate oligomerization catalyst. The sidearm nitrogen is therefore proposed to play a crucial role in determining the propagation process rate, as well as the propagation/termination rate ratio.
Skin responses to topical dehydroepiandrosterone: implications in antiageing treatment? (2010)

These data suggest the possibility that topical DHEA could be used as an efficient and physiological antiageing skin agent.
Effects of Assembly and Mutations Outside the Active Site on the Functional pH Dependence of Escherichia coli Aspartate Transcarbamylase (1996)

Electrostatics are central to the function and regulation of Escherichia coli aspartate transcarbamylase, and modeling has suggested that long range electrostatic effects are likely to be important (Glackin, M. P., McCarthy, M. P., Mallikarachchi, D., Matthew, J. B., and Allewell, N. M. (1989) Proteins Struct. Funct. Genet. 5, 66-77; Oberoi, H., Trikha, J., Yuan, X., and Allewell, N. M. (1995) Proteins Struct. Funct. Genet., in press). To investigate this possibility from an experimental standpoint, we have examined the effects both of assembly and of removing ionizable and polar side chains outside the active site (Glu-50, Tyr-165, and Tyr-240) on the pH dependence of the kinetic parameters of aspartate transcarbamylase. The holoenzyme (c6r6) assembles from three regulatory dimers (r2) and two catalytically active trimers (c3). pH dependences of the enzyme kinetic parameters suggest that the mechanisms of productive binding of L-Asp to the binary complexes of the catalytic subunit (c3) and holoenzyme (c6r6) with carbamyl phosphate are different. In contrast, the Michaelis complex appears similar for both c3 and c6r6, except for pK shifts of approximately 1 pH unit. Results also indicate that the catalytic mechanism of the holoenzyme does not involve reverse protonation, as has recently been proposed for the catalytic trimer (Turnbull, J. L., Waldrop, G. L., and Schachman, H. K. (1992) Biochemistry 31, 6562-6569). The tyrosines at positions 165 and 240 are part of a cluster of interactions that links the catalytic subunits in the T state (the cluc4 interface) and which is disrupted in the T --> R transition. The effects of mutating the two Tyr residues are quite different: Y240F has higher than wild-type activity and affinity over the entire pH range, while Y165F has activity and affinity an order of magnitude lower than wild-type. Removal of the regulatory subunits from Y165F increases activity and affinity and restores the pH dependence of the wild-type catalytic subunit. Like Y165F, E50A has low activity and affinity over the entire pH range. Linkage analysis indicates that there is long range energetic coupling among the active site, the ear subunit interfaces, and residue Y165. The substantial quantitative difference between Y165F and Y240F, both of which are at the c1:c4 interface about 14-16 A from the closest active site, demonstrates specific path dependence, as opposed to general distance dependence, of interactions between this interface and the active site.
Graceful adaptation of guaranteed performance service connections (2002)

Most of the solutions proposed to support guaranteed performance communication services in a packet-switching network adopt a connection-oriented and reservation-oriented approach. In this approach, the resource allocation and route selection decisions are made during connection establishment on the basis of the current resource availability and real-time network load, and are usually kept for the duration of the connection's life time. However, such an approach shows two major limitations: first, the communication service provided is usually fixed, with limited or no capability of adapting to dynamic changes in the clients' requirements; second, a low utilization of the network may be observed. In the paper, the authors present a flexible management scheme that allows graceful adaptation of guaranteed performance service connections. Mechanisms have been devised to allow changing of the trade and performance parameters of a real-time connection during its lifetime. These mechanisms, together with an adaptation policy, can make more efficient use of the network resources by performing cooperative, consenting, high-level multiplexing. the authors distinguish between two types of adaptation: client initiated adaptation and network initiated adaptation. They give examples for both types and present results from simulation experiments to show the effectiveness of the approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Magnetic Susceptibility of the Iron in Ferrohemoglobin (1938)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Magnetic Susceptibility of the Iron in FerrohemoglobinDonald S. Taylor and Charles D. CoryellCite this: J. Am. Chem. Soc. 1938, 60, 5, 1177–1181Publication Date (Print):May 1, 1938Publication History Published online1 May 2002Published inissue 1 May 1938https://pubs.acs.org/doi/10.1021/ja01272a051https://doi.org/10.1021/ja01272a051research-articleACS PublicationsRequest reuse permissionsArticle Views233Altmetric-Citations40LEARN 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
Identification of the amino acid in the human immunodeficiency virus type 1 reverse transcriptase involved in the pyrophosphate binding of antiviral nucleoside triphosphate analogs and phosphonoformate (1993)

A recombinant clone of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) with reduced sensitivity to 3'-azido-3'-deoxythymidine 5'-triphosphate (AZTTP) and phosphonoformate (PFA), a pyrophosphate analog, has been obtained from the RNA of HTLV-IIIB infected cells using the polymerase chain reaction. The mutant HIV-1 RT retained polymerase activity and was cross-resistant to triphosphate forms of other nucleoside analogs including 2',3'-dideoxycytidine 5'-triphosphate, 2',3'-dideoxyadenosine 5'-triphosphate, and 3'-deoxy-2',3'-didehydrothymidine 5'-triphosphate (D4TTP), but remained sensitive to the non-nucleoside HIV-1 RT inhibitors, such as nevirapine and TIBO R82150. Sequence analysis of the mutant HIV-1 RT revealed a single amino acid substitution (Val-->Ala) at amino acid 90. The substitution of amino acid 90 by the closely related amino acids, such as Thr and Gly, also showed decreased sensitivity to AZTTP, D4TTP, and PFA. All these mutations at amino acid 90 also caused an alteration of Km for thymidine triphosphate. These results suggest that Val at this site plays a role in determining the interaction of the HIV-1 RT enzyme with the pyrophosphate group of deoxynucleoside triphosphate (dNTP) and that the hydrophobicity of the amino acid at this position was the most important determinant in the binding of HIV-1 RT to dNTP.
Stimulation of c-myc oncogene expression associated with estrogen-induced proliferation of human breast cancer cells. (1987)

Regulation of c-myc expression is known to be sensitive to a variety of mitogenic stimuli in various cell types. Since estrogen is a well documented mitogen of estrogen-responsive human breast cancer (HBC) cells, we studied the influence of estradiol and its antagonist tamoxifen on the expression of c-myc in HBC cell lines. Using Northern hybridization analysis, we monitored the accumulation of c-myc mRNA in a number of HBC cell lines. The cell lines studied included the estrogen-responsive, estrogen receptor positive (ER+) MCF-7, T-47D, the nonresponsive, estrogen receptor negative (ER-) MDA-MB-231, BT-20, and a nontumorous breast cell line, HBL-100. The effects of endogenous estrogen were minimized by culturing the cells in medium containing 10% (v/v) charcoal-treated fetal bovine serum and tamoxifen (10(-6) M) for 48 h prior to estradiol (10(-7) M) treatment. In the ER+ cell lines the addition of estradiol resulted in a noticeable increase in c-myc expression after 15 min with a maximal (greater than 10-fold) induction in 1-2 h. In the ER- cell lines the level of c-myc mRNA was high and was unaffected by estrogen or tamoxifen; in the ER- cancer cell lines, neither amplification nor rearrangement of the c-myc gene was observed. In contrast, the expression of another oncogene, c-H-ras, remained constant in both ER+ and ER- cell lines and was insensitive to estrogen and antiestrogen. These results suggest that regulation of c-myc expression may be an important step in estrogen-induced proliferation of HBC cells.
Serum Levels of Advanced Glycation Endproducts and Other Markers of Protein Damage in Early Diabetic Nephropathy in Type 1 Diabetes (2012)

Complex processes influence levels of plasma protein damage and related proteolysis product free adducts in type 1 diabetes and microalbuminuria. The effects observed point to the possibility that patients who have efficient mechanisms of disposal of damaged proteins might be at an increased risk of developing microalbuminuria but not early renal function decline. The findings support the concept that the mechanisms responsible for microalbuminuria may differ from the mechanisms involved in the initiation of early renal function decline.
<b>Three conserved consensus sequences identify the NAD‐binding site of ADP‐ribosylating enzymes, expressed by eukaryotes, bacteria and T‐even bacteriophages</b> (1996)

It has been previously reported that the three-dimensional structures of the NAD-binding and catalytic site of bacterial toxins with ADP-ribosylating activity are superimposable, and that the key amino acids for the enzymatic activity are conserved. The model includes an NAD-binding and catalytic site formed by an alpha-helix bent over a beta-strand, surrounded by two beta-strands bearing a Glu and a His, or Arg, that are required for catalysis. We show here that the model can be extended to comprise all proteins with ADP-ribosylating activity known to date, including all eukaryotic mono- and poly-ADP-ribosyltransferases, the bacterial ADP-ribosylating enzymes which do not have toxic activity, and the analogous enzymes encoded by T-even bacteriophages. We show that, in addition to the common Glu and Arg/His amino acids previously identified, the conserved motifs can be extended as follows: (i) the Arg/His motif is usually arom-His/Arg (where 'arom' is an aromatic residue); (ii) in the sequences of the CT group the beta-strand forming part of the 'scaffold' of the catalytic cavity has an arom-ph-Ser-Thr-Ser-ph consensus (where 'ph' represents a hydrophobic residue); and (iii) the motif centered in the key glutamic residue is Glu/Gin-X-Glu; while (iv) in the sequences of the DT group the NAD-binding motif is Tyr-X10-Tyr. We believe that the model proposed not only accounts for all ADP-ribosylating proteins known to date, but it is likely to fit other enzymes (currently being analysed) which possess such an activity.
Diode laser-based air mass flux sensor for subsonic aeropropulsion inlets (1996)

An optical air mass flux sensor based on a compact, room-temperature diode laser in a fiber-coupled delivery system has been tested on a full-scale gas turbine engine. The sensor is based on simultaneous measurements of O2 density and Doppler-shifted velocity along a line of sight across the inlet duct. Extensive tests spanning engine power levels from idle to full afterburner demonstrate accuracy and precision of the order of 1–2% of full scale in density, velocity, and mass flux. The precision-limited velocity at atmospheric pressure was as low as 40 cm/s. Multiple data-reduction procedures are quantitatively compared to suggest optimal strategies for flight sensor packages.
Multiple myeloma and persistence of drug resistance in the age of novel drugs (Review) (2016)

Multiple myeloma (MM) is a mature B cell neoplasm that results in multi-organ failure. The median age of onset, diverse clinical manifestations, heterogeneous survival rate, clonal evolution, intrinsic and acquired drug resistance have impact on the therapeutic management of the disease. Specifically, the emergence of multidrug resistance (MDR) during the course of treatment contributes significantly to treatment failure. The introduction of the immunomodulatory agents and proteasome inhibitors has seen an increase in overall patient survival, however, for the majority of patients, relapse remains inevitable with evidence that these agents, like the conventional chemotherapeutics are also subject to the development of MDR. Clinical management of patients with MM is currently compromised by lack of a suitable procedure to monitor the development of clinical drug resistance in individual patients. The current MM prognostic measures fail to pick the clonotypic tumor cells overexpressing drug efflux pumps, and invasive biopsy is insufficient in detecting sporadic tumors in the skeletal system. This review summarizes the challenges associated with treating the complex disease spectrum of myeloma, with an emphasis on the role of deleterious multidrug resistant clones orchestrating relapse.
Coordinated plant defense responses in <i>Arabidopsis</i> revealed by microarray analysis (2000)

Disease resistance is associated with a plant defense response that involves an integrated set of signal transduction pathways. Changes in the expression patterns of 2,375 selected genes were examined simultaneously by cDNA microarray analysis in Arabidopsis thaliana after inoculation with an incompatible fungal pathogen Alternaria brassicicola or treatment with the defense-related signaling molecules salicylic acid (SA), methyl jasmonate (MJ), or ethylene. Substantial changes (up- and down-regulation) in the steady-state abundance of 705 mRNAs were observed in response to one or more of the treatments, including known and putative defense-related genes and 106 genes with no previously described function or homology. In leaf tissue inoculated with A. brassicicola, the abundance of 168 mRNAs was increased more than 2.5-fold, whereas that of 39 mRNAs was reduced. Similarly, the abundance of 192, 221, and 55 mRNAs was highly (>2.5-fold) increased after treatment with SA, MJ, and ethylene, respectively. Data analysis revealed a surprising level of coordinated defense responses, including 169 mRNAs regulated by multiple treatments/defense pathways. The largest number of genes coinduced (one of four induced genes) and corepressed was found after treatments with SA and MJ. In addition, 50% of the genes induced by ethylene treatment were also induced by MJ treatment. These results indicated the existence of a substantial network of regulatory interactions and coordination occurring during plant defense among the different defense signaling pathways, notably between the salicylate and jasmonate pathways that were previously thought to act in an antagonistic fashion.
Electrotransformation of Brevibacterium lactofermentum and Corynebacterium glutamicum: growth in tween 80 increases transformation frequencies (1989)

Cells from mid-exponential cultures of Brevibacterium lactofermentum were successfully transformed with pUL340 plasmid DNA using a standard (BioRad) electroporation protocol. However, growth in the presence of glycine plus tween 80 greatly increased the transformation frequencies and selecting transformants on an osmotically-protective medium resulted in further improvements. Under these optimal conditions, 4 × 107 transformants/µg DNA were isolated per 109 cells electroporated. Similar transformation frequencies were obtained for Corynebacterium glutamicum when tween 80 was added to the growth medium in addition to glycine and isonicotinic acid hydrazide, conditions which had been found previously to be essential for obtaining significant electrotransformation levels in this species.
Fibrin Targeting of Echogenic Liposomes with Inactivated Tissue Plasminogen Activator (2008)

Fibrin-specific molecular targeting strategies are desirable for site-specific imaging and treatment of late stage atheroma, but fibrin-specific antibodies are difficult to produce and present immunogenicity problems. Tissue plasminogen activator (tPA) is an endogenous protein that has been shown to bind fibrin with high affinity and may circumvent antibody difficulties. Use of tPA-derived proteins or peptides, however, requires that the plasminogen-activating proteolytic activity be neutralized or removed. As an initial step in determining the feasibility of this targeting strategy, human recombinant tPA (Activase) was irreversibly inhibited with D-phe-L-pro-L-arg-chloromethyl ketone (PPACK) and conjugated to intrinsically echogenic liposomes (ELIP) by a thioether coupling protocol. Fibrin-binding affinities were assessed with a novel two-stage fibrin pad ELISA. We achieved 95-99% inactivation, while retaining both tPA fibrin-binding activities of K(D) approximately 2 nM and 33 nM. Thermodynamic analysis of the PPACK-inactivated tPA (tPA(P)) revealed highly exothermic interactions, indicative of ionic associations, especially for the higher affinity. The conjugation efficiency of tPA(P) to ELIP was within the range of that previously achieved for IgG and exhibited satisfactory fibrin targeting, characterized by striking increases of enthalpy and entropy increments. Evidence for coupling of noncovalent association energetics with the phosphatidylethanolamine major phase transition, observed in previous IgG antibody conjugations, was also evident in this case, but the nature of the transduction mechanism was different. These results demonstrate that tPA-derived components lacking proteolytic activity can be employed as fibrin-targeting agents for delivery of therapeutic and diagnostic formulations.
Purification and characterization of a brain-specific multifunctional calmodulin-dependent protein kinase from rat cerebellum. (1992)

A brain-specific multifunctional calmodulin-dependent protein kinase, calmodulin-dependent protein kinase IV, which exhibited characteristic properties quite different from those of calmodulin-dependent protein kinase II, was purified approximately 230-fold from rat cerebellum. The purified preparation gave two protein bands with molecular weights of 63,000 (alpha) and 66,000 (beta) on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, both of which showed protein kinase activity as examined by the activity gel method. The molecular weight of the enzyme was estimated as about 67,000 from sedimentation coefficient (3.2 S) and Stokes radius (50 A), indicating a monomeric structure of the enzyme. The enzyme phosphorylated smooth muscle myosin light chain, synapsin I, microtubule-associated protein 2, tau protein, myelin basic protein, histone H1, and tyrosine hydroxylase in a Ca2+/calmodulin dependent manner, suggesting that the enzyme is a multifunctional calmodulin-dependent protein kinase capable of phosphorylating a large number of substrates. A synthetic peptide, Lys-Ser-Asp-Gly-Gly-Val-Lys-Lys-Arg-Lys-Ser-Ser-Ser-Ser, was found to be a specific substrate for this kinase and, using this peptide as substrate, the distribution of the enzyme activity in various rat tissues was examined. The activity was found in cerebral cortex, brain stem, and cerebellum, most abundantly in cerebellum, but other tissues tested, including liver, spleen, kidney, lung, heart, skeletal muscle, and adrenal gland showed very little activity.