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At least 235 records · Page 13

Photostable and efficient upconverting nanocrystal-based chemical sensors

Chemical sensing in living systems demands optical sensors that are bright, stable, and sensitive to the rapid dynamics of chemical signaling. Lanthanide-doped upconverting nanoparticles (UCNPs) efficiently convert near infrared (NIR) light to higher energy emission and allow biological systems to be imaged with no measurable background or photobleaching, and with reduced scatter for subsurface experiments. Despite their advantages as imaging probes, UCNPs have little innate chemical sensing ability and require pairing with organic fluorophores to act as biosensors, although the design of stable UCNP-fluorophore hybrids with efficient upconverted energy transfer (UET) has remained a challenge. Here, we report Yb 3+ - and Er 3+ -doped UCNP-fluorophore conjugates with UET efficiencies up to 88%, and photostabilities 100-fold greater by UET excitation than those of the free fluorophores under direct excitation. Despite adding distance between Er 3+ donors and organic acceptors, thin inert shells significantly enhance overall emission without compromising UET efficiency. This can be explained by the large increase in quantum yield of Er 3+ donors at the core/shell interface and the large number of fluorophore acceptors at the surface. Sensors excited by UET show increases in photostability well beyond those reported for other methods for increasing the longevity of organic fluorophores, and those covalently attached to UCNP surface polymers show greater chemical stability than those directly coordinated to the nanocrystal surface. Furthermore by conjugating other fluorescent chemosensors to UCNPs, these hybrids may be extended to a series of NIR-responsive biosensors for quantifying the dynamic chemical populations critical for cell signaling.

36 MATERIALS SCIENCE↗

Biochemical characterization of nuclear receptors for vitamin D{sub 3} and glucocorticoids in prostate stroma cell microenvironment

Highlights: {yields} Fibroblasts from benign and carcinoma-associated stroma were biochemically characterized for VDR and GR function as transcription factors in prostate stroma cell microenvironment. {yields} Decreased SRC-1/CBP coactivators recruitment to VDR and GR may result in hormone resistance to 1,25D{sub 3} in stromal cell microenvironment prostate cancer. {yields} 1a,25-Dyhidroxyvitamin D{sub 3} (1,25D{sub 3}) and glucocorticoids, either alone or in combination, may not be an alternative for 'some' advanced prostate cancers that fails androgen therapies. -- Abstract: The disruption of stromal cell signals in prostate tissue microenvironment influences the development of prostate cancer to androgen independence. 1{alpha},25-Dihydroxyvitamin D{sub 3} (1,25D{sub 3}) and glucocorticoids, either alone or in combination, have been investigated as alternatives for the treatment of advanced prostate cancers that fails androgen therapies. The effects of glucocorticoids are mediated by the intracellular glucocorticoid receptor (GR). Similarly, the effect of 1,25D{sub 3} is mediated by the 1,25D{sub 3} nuclear receptor (VDR). In this study, fibroblasts from benign- (BAS) and carcinoma-associated stroma (CAS) were isolated from human prostates to characterize VDR and GR function as transcription factors in prostate stroma. The VDR-mediated transcriptional activity assessed using the CYP24-luciferase reporter was limited to 3-fold induction by 1,25D{sub 3} in 9 out of 13 CAS (70%), as compared to >10-fold induction in the BAS clinical sample pair. Expression of His-tagged VDR (Ad-his-VDR) failed to recover the low transcriptional activity of the luciferase reporter in 7 out of 9 CAS. Interestingly, expression of Ad-his-VDR successfully recovered receptor-mediated induction in 2 out of the 9 CAS analyzed, suggesting that changes in the receptor protein itself was responsible for decreased response and resistance to 1,25D{sub 3} action. Conversely, VDR-mediated transcriptional activity was more efficient in 4 out of 13 CAS (30%), as compared to the BAS sample pair. Consistent with the reduced response to 1,25D{sub 3} observed in CAS, chromatin immunoprecipitation (ChIP) assays indicated decreased recruitment of coactivators SRC-1/CBP, without major changes in the recruitment of VDR to the CYP24 promoter. In addition, we observed that GR-mediated transcriptional activity was also altered in CAS, as compared to BAS. Disruption of coactivators SRC-1/CBP recruitment may promote hormone resistance in CaP, and highlights the relevance of molecular diagnosis and drug design in tumor cell microenvironment.

60 APPLIED LIFE SCIENCES↗

Second Generation Grp94-Selective Inhibitors Provide Opportunities for the Inhibition of Metastatic Cancer

Glucose regulated protein 94 (Grp94) is the endoplasmic reticulum (ER) resident isoform of the 90 kDa heat shock protein (Hsp90) family and its inhibition represents a promising therapeutic target for the treatment of many diseases. Modification of the first generation cis-amide bioisostere imidazole to alter the angle between the resorcinol ring and the benzyl side chain via cis-amide replacements produced compounds with improved Grp94 affinity and selectivity. Structure–activity relationship studies led to the discovery of compound 30, which exhibits 540 nm affinity and 73-fold selectivity towards Grp94. Grp94 is responsible for the maturation and trafficking of proteins associated with cell signaling and motility, including select integrins. The Grp94-selective inhibitor 30 was shown to exhibit potent anti-migratory effects against multiple aggressive and metastatic cancers.

59 BASIC BIOLOGICAL SCIENCES↗

Automated Immobilized Metal Affinity Chromatography System for Enrichment of Escherichia coli Phosphoproteome

Enrichment of bacterial phosphopeptides is an essential step prior to bottom-up mass spectrometry-based analysis of the phosphoproteome, which is fundamental to understanding the role of phosphoproteins in cell signaling and regulation of protein activity. We developed an automated IMAC system to enrich strong cation exchange-fractionated phosphopeptides from the soluble proteome of Escherichia coli MG1655 grown on minimal medium. Initial demonstration of the system resulted in identification of 75 phosphopeptides covering 52 phosphoproteins. Consistent with previous studies, many of these phosphoproteins are involved in the carbohydrate portion of central metabolism. The automated system utilizes a large capacity IMAC column that can effectively enrich phosphopeptides from a bacterial sample by increasing peptide loading and reducing the wash time. An additional benefit of the automated IMAC system is reduced labor and associated costs.

Environmental Molecular Sciences Laboratory↗

Intermolecular versus intramolecular interactions of the vinculin binding site 33 of talin

The cytoskeletal proteins talin and vinculin are localized at cell-matrix junctions and are key regulators of cell signaling, adhesion, and migration. Talin couples integrins via its FERM domain to F-actin and is an important regulator of integrin activation and clustering. The 220 kDa talin rod domain comprises several four- and five-helix bundles that harbor amphipathic {alpha}-helical vinculin binding sites (VBSs). In its inactive state, the hydrophobic VBS residues involved in binding to vinculin are buried within these helix bundles, and the mechanical force emanating from bound integrin receptors is thought necessary for their release and binding to vinculin. The crystal structure of a four-helix bundle of talin that harbors one of these VBSs, coined VBS33, was recently determined. Here we report the crystal structure of VBS33 in complex with vinculin at 2 {angstrom} resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 {alpha}-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle.

59 BASIC BIOLOGICAL SCIENCES↗

Ca X ML: Chemistry‐informed machine learning explains mutual changes between protein conformations and calcium ions in calcium‐binding proteins using structural and topological features

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of Ca X ML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design, synthesis, and cytostatic activity of novel pyrazine sorafenib analogs

The current study is focused on a series of sorafenib analogs as potential antitumor agents. We have designed and synthesized nine novel pyrazine analogs 6a–i differing in amide and/or urea regions. Two alternative strategies for the preparation of title compounds were applied. The first strategy involved ether formation between 4-hydroxyphenyl urea 3 and 5-chloro-pyrazine-2-carboxamides 4. In the second strategy, ether functionality was introduced in the molecule before urea moiety and included preparation of 5-(4-aminophenoxy)-N-alkylpyrazine-2-carboxamides 5 and their reaction with 4-chloro-3-(fluoromethyl)phenyl isocyanate. Cytostatic activity of the title compounds was evaluated in vitro against a panel of cancer cell lines. Most of the tested compounds showed strong antiproliferative activity in the low micromolar range. 5-/4-[3-(4-chloro-3-trifluoromethyl-phenyl)-ureido]-phenoxy/-pyrazine-2-carboxylic acid (4-chloro-3-trifluoromethylphenyl)-amide (6g) was the most active compound (IC{sub 50} 0.9–7.5 μM) and showed comparable or stronger activity than sorafenib, but also similar cytotoxicity to normal human fibroblast cells. Two compounds, namely, 5-/4-[3-(4-bromophenyl)-ureido]-phenyloxy/-pyrazine-2-carboxylic acid cyclopentylamide (6c) and 5-/4-[3-(4-chloro-3-trifluoromethyl-phenyl)-ureido]-phenoxy/-pyrazine-2-carboxylic acid cyclopentylamide (6h), exerted cytostatic activities that surpassed the effects observed with sorafenib in three cancer cell lines (HepG2, HeLa, A549, IC{sub 50} 0.6–0.9 μM). Similar to sorafenib, compound 6h proved to be cytotoxic to normal human fibroblast cells, whereas compound 6c did not diminish proliferative capacity of these cells and could be regarded as the most promising derivative. Additional biological studies on the c-Raf activity using Western blot method revealed that antiproliferative activity of 6h could be at least partially attributed to its inhibitory effect on c-Raf activation similar to sorafenib. In contrast, 6c did not inhibit the activity of c-Raf, which implies that other cell signaling pathways govern its antiproliferative effects. Taking into account structural differences between compounds 6c and 6h, it is plausible to believe that the substituent in urea part of the molecule is essential for the interaction with c-Raf.

60 APPLIED LIFE SCIENCES↗

Recent Advances in Copper Intercalators as Anticancer Agents

Copper is a part of various enzymes and helps them to function properly. It can be effectively used to produce promising anticancer drugs and presently, many studies are being pursued worldwide on the development of copper-based complexes as potential anticancer drugs. Herein, we briefly discuss the importance of reactive oxygen species in biological applications and copper(II) complexes as anticancer drugs. The anti-angiogenic properties of mono-nuclear copper(II) complexes have been demonstrated by in vivo chick embryo angiogenesis analysis. The plausible mechanism behind anticancer activity of these complexes is by the formation of excessive intracellular Reactive Oxygen Species (ROS). ROS is a composite term used for oxygen derivative non-radicals and free radicals of highly reactive components, that enhances the killing response of immune cells to microbial invasion. Previous reports have shown that ROS plays an important role as a messenger in cell cycling and normal cell signal transduction. .

60 APPLIED LIFE SCIENCES↗

Elamipretide effects on the skeletal muscle phosphoproteome in aged female mice

The age-related decline in skeletal muscle mass and function is known as sarcopenia. Sarcopenia progresses based on complex processes involving protein dynamics, cell signaling, oxidative stress, and repair. We have previously found that 8-week treatment with elamipretide improves skeletal muscle function, reverses redox stress, and restores protein S-glutathionylation changes in aged female mice. This study tested whether 8-week treatment with elamipretide also affects global phosphorylation in skeletal muscle consistent with functional improvements and S-glutathionylation. Using female 6–7-month-old mice and 28–29-month-old mice, we found that phosphorylation changes did not relate to S-glutathionylation modifications, but that treatment with elamipretide did partially reverse age-related changes in protein phosphorylation in mouse skeletal muscle.

59 BASIC BIOLOGICAL SCIENCES↗

Chapter 10: Advances in Protein Engineering and its Application in Synthetic Biology

Protein engineering has been used successfully in fields ranging from medicine to food science to biofuels. Applications of protein engineering include developing antiviral peptides or other protein therapeutics, antibody engineering, designing protein-based logic circuits, engineering enzymes to be more specific or to function under industrially relevant conditions such as at higher temperatures or high/low pH, modifying cell signaling or regulatory functions, and so on. Advances in recombinant DNA, "omics," and CRISPR-Cas (clustered regularly interspaced short palindromic repeats and its associated proteins) technologies, combined with high-throughput screening facilities, will lead to improved methods for protein engineering, enabling easy modification of more proteins/enzymes for new specific applications. New methods for rational design, directed evolution, and computer-aided protein design will further accelerate the speed of protein evolution and expand the scope for protein engineering. In this chapter we discuss general protein engineering strategies and advances in engineering proteins with desired functions, focusing on the "design" and "build" part of the design-build-test-learn cycle.

BIOMASS FUELS↗

Applications of NMR and computational methodologies to study protein dynamics

The overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

High inorganic phosphate causes DNMT1 phosphorylation and subsequent fibrotic fibroblast activation

Phosphate is an essential constituent of critical cellular functions including energy metabolism, nucleic acid synthesis and phosphorylation-dependent cell signaling. Increased plasma phosphate levels are an independent risk factor for lowered life-expectancy as well as for heart and kidney failure. Nevertheless, direct cellular effects of elevated phosphate concentrations within the microenvironment are poorly understood and have been largely neglected in favor of phosphor-regulatory hormones. Because interstitial fibrosis is the common determinant of chronic progressive kidney disease, and because fibroblasts are major mediators of fibrogenesis, we here explored the effect of high extracellular phosphate levels on renal fibroblasts. We demonstrate that high inorganic phosphate directly induces fibrotic fibroblast activation associated with increased proliferative activity, increased expression of α-smooth muscle actin and increased synthesis of type I collagen. We further demonstrate that such fibroblast activation is dependent on phosphate influx, aberrant phosphorylation of DNA methyltransferase DNMT1 and aberrant CpG island promoter methylation. In summary, our studies demonstrate that elevated phosphate concentrations induce pro-fibrotic fibroblast activation independent of phospho-regulatory hormones. - Highlights: • We exposed human kidney fibroblasts to media containing 1 mM or 3 mM phosphate. • Increased phosphate influx causes phosphorylation of DNA methyltransferase Dnmt1. • Phosphorylated Dnmt1 causes promoter methylation and transcriptional silencing of RASAL1. • Depletion of RASAL1 causes increased intrinsic Ras-GTP activity and fibroblast activation. • Inorganic phosphate causes fibroblast activation independent of phospho-regulatory hormones.

60 APPLIED LIFE SCIENCES↗

Nicorandil alleviates myocardial injury and post-infarction cardiac remodeling by inhibiting Mst1

Highlights: • Nicorandil upregulates cardiomyocyte autophagy, while reduces cardiomyocytes apoptosis. • Nicorandil inhibits left ventricular remodeling and cardiac dysfunction in mice with myocardial infarction (MI). • Mst1 serves as a downstream regulator of nicorandil. Cardiomyocyte autophagy and apoptosis are crucial events underlying the development of cardiac abnormalities and dysfunction after myocardial infarction (MI). A better understanding of the cell signaling pathways involved in cardiac remodeling may support the development of new therapeutic strategies for the treatment of heart failure (HF) after MI.

60 APPLIED LIFE SCIENCES↗

Lifetime of actin-dependent protein nanoclusters

Protein nanoclusters (PNCs) are dynamic collections of a few proteins that spatially organize in nanometer-length clusters. PNCs are one of the principal forms of spatial organization of membrane proteins, and they have been shown or hypothesized to be important in various cellular processes, including cell signaling. PNCs show remarkable diversity in size, shape, and lifetime. In particular, the lifetime of PNCs can vary over a wide range of timescales. The diversity in size and shape can be explained by the interaction of the clustering proteins with the actin cytoskeleton or the lipid membrane, but very little is known about the processes that determine the lifetime of the nanoclusters. In this paper, using mathematical modeling of the cluster dynamics, we model the biophysical processes that determine the lifetime of actin-dependent PNCs. In particular, we investigated the role of actin aster fragmentation, which had been suggested to be a key determinant of the PNC lifetime, and we found that it is important only for a small class of PNCs. A simple extension of our model allowed us to investigate the kinetics of protein-ligand interaction near PNCs. We found an anomalous increase in the lifetime of ligands near PNCs, which agrees remarkably well with experimental data on RAS-RAF kinetics. In particular, analysis of the RAS-RAF data through our model provides falsifiable predictions and novel hypotheses that will not only shed light on the role of RAS-RAF kinetics in various cancers, but also will be useful in studying membrane protein clustering in general.

59 BASIC BIOLOGICAL SCIENCES↗

Quantitative site-specific reactivity profiling of S-nitrosylation in mouse skeletal muscle using cysteinyl peptide enrichment coupled with mass spectrometry

S-nitrosylation (SNO) is an important reversible thiol oxidation event that has been increasingly recognized for its role in cell signaling. While many proteins susceptible to S-nitrosylation have been reported, site-specific identification of physiologically relevant SNO modifications remains an analytical challenge due to the low-abundance and labile nature of the modification. Herein we present further improvement and optimization of the recently reported, resin-assisted cysteinyl peptide enrichment protocol for SNO identification and the extension of this application to mouse skeletal muscle to identify specific sites sensitive to S-nitrosylation by quantitative reactivity profiling. The results of our data indicate that the protein- and peptide-level enrichment protocols provide comparable specificity and coverage of SNO-peptide identifications. S-nitrosylation reactivity profiling was performed by quantitatively comparing the site-specific SNO modification levels in samples treated with S-nitrosoglutathione (GSNO), an NO donor, at two different physiologically relevant concentrations (i.e., 10 μM and 100 μM). The reactivity profiling experiments overall identified 489 SNO-modified cysteine sites from 197 proteins with the specificity of 95.2% at the unique-peptide-level based on the percentage of Cys-peptides. Among these sites, 260 sites from 135 proteins were observed with relatively high reactivity to S-nitrosylation; such SNO-sensitive sites are more likely to be physiologically relevant. Many of the SNO-sensitive proteins are preferentially localized in mitochondria, contractile fiber and actin cytoskeleton, suggesting the susceptibility of these subcellular compartments to redox regulation. Moreover, the SNO-sensitive proteins seem to be primarily involved in metabolic pathways, including TCA cycle, glycolysis/gluconeogenesis, glutathione metabolism, and fatty acid metabolism, suggesting the importance of redox regulation in muscle metabolism and insulin action.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mass spectrometry structural analysis of intrinsically disordered phosphoproteins

Phosphorylation is a ubiquitous protein modification that is known to play important roles in many biological phenomena including cell signaling, the opening and closing of membrane protein channels, and even triggering of amyloid protein aggregation. Despite the effects phosphorylation has on protein function, the impact phosphorylation has on the structure of proteins is not well understood. Here, to determine how phosphorylation affects the structure of proteins, top-down mass spectrometry (TD-MS) and ion mobility-mass spectrometry (IM-MS) were performed on various phosphorylated proteins and their dephosphorylated proteoforms. TD-MS with collision- and electron-based fragmentation techniques was utilized to locate phosphorylation sites on the intrinsically disordered amyloid proteins β-casein and α-synuclein. TD-MS also provided evidence that alkaline phosphatase dephosphorylates β-casein from the N-terminus to the C-terminus. Furthermore, IM-MS of common phosphorylated proteins such as β-casein, α-casein, ovalbumin, and phosvitin indicates that phosphorylation promotes compaction of protein structure in denaturing as well as native conditions. Increases in abundance of more compact conformers are also observed when the disease related amyloid protein α-synuclein is phosphorylated at serine 129. We interpret the increased abundance of more compact conformers when proteins are phosphorylated as evidence that salt bridges form between negatively charged phosphates and positively charged residues, which alters protein structure. Salt bridge formation due to phosphorylation could be a mechanism for regulating protein function and be responsible for many of the phenomena observed in nature.

Amyloid proteins↗

Variations in the Processing of DNA Double-Strand Breaks Along 60-MeV Therapeutic Proton Beams

Purpose: To investigate the variations in induction and repair of DNA damage along the proton path, after a previous report on the increasing biological effectiveness along clinically modulated 60-MeV proton beams. Methods and Materials: Human skin fibroblast (AG01522) cells were irradiated along a monoenergetic and a modulated spread-out Bragg peak (SOBP) proton beam used for treating ocular melanoma at the Douglas Cyclotron, Clatterbridge Centre for Oncology, Wirral, Liverpool, United Kingdom. The DNA damage response was studied using the 53BP1 foci formation assay. The linear energy transfer (LET) dependence was studied by irradiating the cells at depths corresponding to entrance, proximal, middle, and distal positions of SOBP and the entrance and peak position for the pristine beam. Results: A significant amount of persistent foci was observed at the distal end of the SOBP, suggesting complex residual DNA double-strand break damage induction corresponding to the highest LET values achievable by modulated proton beams. Unlike the directly irradiated, medium-sharing bystander cells did not show any significant increase in residual foci. Conclusions: The DNA damage response along the proton beam path was similar to the response of X rays, confirming the low-LET quality of the proton exposure. However, at the distal end of SOBP our data indicate an increased complexity of DNA lesions and slower repair kinetics. A lack of significant induction of 53BP1 foci in the bystander cells suggests a minor role of cell signaling for DNA damage under these conditions.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Protein design for pathway engineering

Design and construction of biochemical pathways has increased the complexity of biosynthetically-produced compounds when compared to single enzyme biocatalysis. However, the coordination of multiple enzymes can introduce a complicated set of obstacles to overcome in order to achieve a high titer and yield of the desired compound. Metabolic engineering has made great strides in developing tools to optimize the flux through a target pathway, but the inherent characteristics of a particular enzyme within the pathway can still limit the productivity. Thus, judicious protein design is critical for metabolic and pathway engineering. This review will describe various strategies and examples of applying protein design to pathway engineering to optimize the flux through the pathway. The proteins can be engineered for altered substrate specificity/selectivity, increased catalytic activity, reduced mass transfer limitations through specific protein localization, and reduced substrate/product inhibition. Protein engineering can also be expanded to design biosensors to enable high through-put screening and to customize cell signaling networks. These strategies have successfully engineered pathways for significantly increased productivity of the desired product or in the production of novel compounds. (C) 2013 Elsevier Inc. All rights reserved.

Eriksen, DT↗