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PubMed2002

Enzymatic manipulation of DNA-nanomaterial constructs.

The demonstration and control of biofunction between inorganic nanomaterials and biological scaffolding is crucial to the development of the field of biomaterials. Although unique hierarchical structures can be generated, the impact of nanosized materials on the biological activity of DNA-protein interactions is relatively unknown. Using highly selective proteins that induce sequence-specific conformational perturbations within DNA, we demonstrate the absolute maintenance of biofunction for biomaterials composed of duplex DNA appended with 1.4-nm Au particles. Enzyme activity and DNA binding affinities (K(d)) are unaltered by the nanoparticle-DNA conjugates. Our results provide a foundation for interfacing more complex and diverse protein-DNA-systems.

DNA↗

PubMed2004

A wrench-shaped synthetic molecule that modulates a transcription factor-coactivator interaction.

Development of synthetic molecules that provide external control over the transcription of a given gene represents a challenge in medicinal and bioorganic chemistry. Here we report design and analysis of wrenchnolol, a wrench-shaped synthetic molecule that impairs the transcription of the Her2 oncogene by disrupting association of transcription factor ESX with its coactivator Sur-2. The "jaw" part of the compound mimics the alpha-helical interface of the activation domain of ESX, and the "handle" region accepts chemical modifications for a range of analysis. A water-soluble handle permitted NMR study in aqueous solution; a biotinylated handle verified the selectivity of the interaction, and a fluorescent handle confirmed the cell permeability of the compound. The case study of wrenchnolol foreshadows the promise and the challenge of targeting protein-protein interactions in the nucleus and may lead to the development of unique synthetic modulators of gene transcription.

Adamantane↗

PubMed2005

Solution structure of a beta-peptide ligand for hDM2.

We recently reported a beta-peptide foldamer, beta53-1, that folds into a 14-helix in aqueous solution, binds the oncoprotein hDM2 with submicromolar affinity, and potently inhibits the interaction of hDM2 with a peptide derived from the activation domain of p53 (p53AD). Here, we present the solution structure of beta53-1 in methanol. Details of the structure illustrate fundamental and novel elements of beta-peptide folding and recognition. These elements include the detailed arrangement of a complex, 14-helix-stabilizing salt bridge on one helical face, and a unique "wedge into cleft" packing interaction along a second. The structure also reveals how a subtle distortion in the beta53-1 14-helix geometry alters the presentation of its recognition epitope, rendering it particularly well suited for alpha-helix mimicry. The solution structure of beta53-1 demonstrates that well folded beta-peptide oligomers can effectively present an extended, highly variable surface that could be used as a general platform for targeting critical protein-protein interfaces.

Ligands↗

PubMed1999

Expression of trophinin, tastin, and bystin by trophoblast and endometrial cells in human placenta.

Trophinin, tastin, and bystin comprise a complex mediating a unique homophilic cell adhesion between trophoblast and endometrial epithelial cells at their respective apical cell surfaces. In this study, we prepared mouse monoclonal antibodies specific to each of these molecules. The expression of these molecules in the human placenta was examined immunohistochemically using the antibodies. In placenta from the 6th week of pregnancy, trophinin and bystin were found in the cytoplasm of the syncytiotrophoblast in the chorionic villi, and in endometrial decidual cells at the utero placental interface. Tastin was exclusively present on the apical side of the syncytiotrophoblast. Tissue sections were also examined by in situ hybridization using RNA probes specific to each of these molecules. This analysis showed that trophoblast and endometrial epithelial cells at the utero placental interface express trophinin, tastin, and bystin. In wk 10 placenta, trophinin and bystin were found in the intravillous cytotrophoblast, while tastin was not found in the villi. After wk 10, levels of all three proteins decreased and then disappeared from placental villi.

Antibodies, Monoclonal↗

PubMed2004

Physician leadership: enhancing the career development of academic physician administrators and leaders.

As the health care environment grows more complex, there is greater opportunity for physician administrative and management leadership. Although physicians in general, and academic physicians in particular, view management as outside their purview, the increased importance of physician administrative leadership represents an opportunity for academic physicians interested in working at the interface of clinical medicine, health care, finance, and management. These physicians are called academic physician administrators and leaders (APALs). APALs are clinician-administrators whose academic contributions include both scholarly work related to their administrative duties and administrative leadership of academically important programs. However, existing academic career development infrastructure, such as academic promotions, is oriented toward traditional clinician-educator and clinician-researcher faculty. The APAL career path differs from traditional academic pathways because APALs require unique skills, different mentors, and a more expansive definition of academic productivity. This article describes how academic medical institutions could enhance the career development of academic physicians in administrative and leadership positions.

Career Mobility↗

PubMed2005

Preferential recognition of undisruptable dimers of inducible nitric oxide synthase by a monoclonal antibody directed against an N-terminal epitope.

Overproduction of NO by inducible NO synthase (iNOS) has been implicated in the pathogenesis of many diseases. iNOS is active only as a homodimer in which the subunits align in a head-to-head manner, with the N-terminal oxygenase domains forming the dimer interface and a zinc metal center stabilizing the dimer. Thus, dimerization represents a critical locus for therapeutic interventions for regulation of NO synthesis. We have recently shown that intracellular iNOS forms dimers that are "undisruptable (UD)" by heat, SDS, strong denaturants, and/or reducing agents. Our data further suggest that the zinc metal center plays a role in forming and/or stabilizing iNOS undisruptable dimers (UD-dimers). In this study, we show that a mAb directed against a unique epitope at the oxygenase domain of human iNOS preferentially recognizes UD-dimers. This observation has implications for the mechanism of formation and regulation of dimer formation of iNOS. Our data suggest that UD-dimers of iNOS, in spite of SDS-PAGE denaturation, still maintain features of the quaternary structure of iNOS particularly at its N-terminal end and including head-to-head contact of the oxygenase domains.

Animals↗

PubMed1993

The platelet-activating factor acetylhydrolase from human erythrocytes. Purification and properties.

Platelet-activating factor (PAF, 1-O-alkyl-2-acetyl-sn-glycero-3- phosphocholine) is a biologically active phospholipid. Tissues, blood cells, and plasma contain PAF acetylhydrolases (calcium independent phospholipase A2 activities) that catalyze the hydrolysis of phospholipids containing short chain sn-2 acyl groups. They inactivate PAF and thereby determine PAF accumulation. We purified the PAF acetylhydrolase from human erythrocytes 15,600-fold. The enzyme has a molecular weight of 25,000, it behaves as a dimer during gel filtration, and it is a previously uncharacterized cytosolic esterase, as it has a unique amino-terminal sequence. The erythrocyte PAF acetylhydrolase requires the addition of sulfhydryl agents for maximal activity, is inhibited by 5,5'-dithiobis(2-nitrobenzoic acid), NaF, diisopropyl fluorophosphate, diethylpyrocarbonate, p-bromophenacylbromide, and a number of proteases. Antibodies against the purified protein precipitate all PAF hydrolase activity from erythrocyte lysates. The erythrocyte PAF acetylhydrolase is specific for short or oxidized sn-2 acyl residues. It exhibits surface dilution kinetics, suggesting that hydrolysis occurs at lipid interfaces. This suggests that this enzyme acts in vivo as a scavenger of oxidatively fragmented phospholipids that are toxic to the cell.

1-Alkyl-2-acetylglycerophosphocholine Esterase↗

PubMed2006

Effect of sphingomyelin and cholesterol on the interaction of St II with lipidic interfaces.

Sticholysin II (St II) is a cytolysin produced by the sea anemone Stichodactyla helianthus, characterized by forming oligomeric pores in natural and artificial membranes. In the present work the influence of the membrane lipidic components sphingomyelin (SM) and cholesterol (Cho) on binding and functional activity of St II, was evaluated using ELISA, lipid monolayers and liposomes. The aim of this work was to establish the promoting role of Cho and SM, both in St II binding and pore formation efficiency. In general the association (evaluated by ELISA and incorporation to phospholipid monolayers) of St II to lipids mixtures was better than to any one of the single components. Regarding the unique role of SM, it was found that, albeit inefficiently, St II binds to phosphatidylcholine (PC):Cho monolayers and liposomes, and is able to form active pores in these bilayers. The results in monolayers and liposomes show that the presence of SM and large amounts of Cho leads to the highest values of critical pressure and rate of association to monolayers, the most favorable interaction with liposomes, and the fastest rate of pore formation, in spite of the rigidity of the layers as suggested by the high generalized polarization (GP) of Laurdan incorporated to liposomes and FTIR data. Taken together, the present results show that the joint presence of SM and Cho, both in binary and ternary (PC containing) mixtures provide conditions particularly suitable for St II binding and function. We suggest that microdomains present in the bilayers could be important for toxin-membrane association.

Animals↗

PubMed2006

Proteomic analysis of Candida albicans yeast and hyphal cell wall and associated proteins.

Candida albicans is an important human pathogen that causes systemic infections, predominantly among populations with weakened immune systems. The morphological transition from the yeast to the hyphal state is one of the key factors in C. albicans pathogenesis. Owing to their location at the host-pathogen interface, the cell wall and associated proteins are of interest, especially with respect to the yeast to hyphal transition. This study entailed the proteomic analysis of differentially regulated proteins involved in this transition. The protein profiles of C. albicans DTT/SDS-extractible proteins and the cyanogen bromide (CNBr)/trypsin-extractable proteins of a cell wall-enriched fraction from yeast and hyphae were compared. In total, 107 spots were identified from the DTT/SDS-extractible cell wall-enriched fraction, corresponding to 82 unique proteins. Of these DTT/SDS-extractible proteins, 14 proteins were upregulated and 10 were downregulated in response to hyphal induction. Approximately 6-9% of total cell wall-protein-enriched fraction was found to be resistant to DTT/SDS extraction. Analysis of the DTT/SDS-resistant fraction using a CNBr/trypsin extraction resulted in the identification of 29 proteins. Of these, 17 were identified only in the hyphae, four were identified only in the yeast, and eight were identified in both the yeast and hyphae.

Amino Acid Sequence↗

PubMed2001

Factors modulating the epithelial response to toxicants in tracheobronchial airways.

As one of the principal interfaces between the organism and the environment, the respiratory system is a target for a wide variety of toxicants and carcinogens. The cellular and architectural complexity of the respiratory system appears to play a major role in defining the focal nature of the pulmonary response to environmental stressors. This review will address the biological factors that modulate the response of one of the major target compartments within the respiratory system, the tracheobronchial airway tree. Individual airway segments respond uniquely to toxic stress and this response involves not only the target cell population, e.g. epithelium, but also other components of the airway wall suggesting a trophic interaction within all components of the airway wall in maintaining steady state and responding to injury. A number of biological factors modulate the nature of the response, including: (1) metabolic potential at specific sites for activation and detoxification; (2) the nature of the local inflammatory response; (3) age of the organism at the time of exposure; (4) gender of the exposed organism; (5) history of previous exposure; and (6) species and strain of the organism exposed.

Aging↗

PubMed2005

Thermoplastic elastomer gels: an advanced substrate for microfluidic chemical analysis systems.

We demonstrate the use of thermoplastic elastomer gels as advanced substrates for construction of complex microfluidic networks suitable for use in miniaturized chemical analysis systems. These gels are synthesized by combining inexpensive polystyrene-(polyethylene/polybutylene)-polystyrene triblock copolymers with a hydrocarbon extender oil for which the ethylene/butylene midblocks are selectively miscible. The insoluble styrene end blocks phase separate into localized nanodomains, resulting in the formation of an optically transparent, viscoelastic, and biocompatible gel network that is melt-processable at temperatures in the vicinity of 100 degrees C. This unique combination of properties allows microfluidic channels to be fabricated in a matter of minutes by simply making impressions of the negative relief structures on heated master molds. Melt processability allows multiple impressions to be made against different masters to construct complex geometries incorporating multi-height features within the same microchannel. Intricate interconnected multilayered structures are also easily fabricated owing to the ability to bond and seal multiple layers by briefly heating the material at the bond interface. Thermal and mechanical properties are tunable over a wide range through proper selection of gel composition.

Biocompatible Materials↗

PubMed2003

The alphavbeta5 integrin of hematopoietic and nonhematopoietic cells is a transduction receptor of RGD-4C fiber-modified adenoviruses.

Epithelial and endothelial cells expressing the primary Coxsackie virus B adenovirus (Ad) receptor (CAR) and integrin coreceptors are natural targets of human Ad infections. The fiber knob of species A, C, D, E and F Ad serotypes binds CAR by mimicking the CAR-homodimer interface, and the penton base containing arginine-glycine-aspartate (RGD) motifs binds with low affinity to alphav integrins inducing cell activation. Here, we generated seven different genetically modified Ad vectors with RGD sequences inserted into the HI loop of fiber knob. All mutants bound and infected CAR and alphav integrin-positive epithelial cells with equal efficiencies. However, the Ads containing two additional cysteines, both N and C terminals of the RGD sequence (RGD-4C), were uniquely capable of transducing CAR-less hematopoietic and nonhematopoietic human tumor cell lines and primary melanoma cells. Both binding and transduction of RGD-4C Ad were blocked by soluble RGD peptides. Flow cytometry of cell surface integrins and virus binding to CAR-less cells in the presence of function-blocking anti-integrin antibodies indicated that the alphavbeta5 integrin, but not alphavbeta3, alphaIIbbeta3 or beta1,alpha5 or alpha6-containing integrins served as a functional transduction receptor of the RGD-4C Ads. However, in cells with low levels of alphavbeta5 integrin, the function-blocking anti-alphavbeta5 antibodies were not effective, unlike soluble RGD peptides. Collectively, our data demonstrate that the alphavbeta5 integrin is a functional transduction receptor of RGD-4C Ads in the absence of CAR, and that additional RGD receptors are targets of these viruses. The RGD-4C vectors further extend the tropism of Ads towards potential human therapies.

Adenoviridae↗

PubMed2004

The interface between the practice of medical genetics and human genetic research: what every genetic counselor needs to know.

Genetic counselors have historically used human genetic research as an advanced information resource for their patients. Most commonly, this has been via access to information provided by gene identification studies in advance of commercial testing. More recently genetic counselors have been participating in human genetic research studies as part of the investigative team. This review provides a framework to help genetic counselors in research and clinical practice understand the historical perspectives, ethical principles, and federal regulations that govern the current practice of human subject research. Special consideration is given to the IRB process and unique issues in human genetic research. This overview is intended to help improve the ability of genetic counselors to act as advocates for their patients.

Genetic Counseling↗

PubMed2006

Rb at the interface between cell cycle and apoptotic decisions.

The retinoblastoma (RB) gene was the first tumor suppressor to be identified, and it continues to be the subject of intense scientific interest. Not only is the RB gene mutated in the rare eye tumor and some other cancers, the Rb protein is functionally inactivated in virtually all human cancers, suggesting that it plays a general role in cellular homeostasis. Rb initially was envisaged as a simple 'on-off' regulator of the cell cycle, and this function was thought to account for its role as a tumor suppressor. Subsequently, however, closer scrutiny revealed unexpected and complex properties of Rb that together contribute to the unique role of Rb in cell biology. For example, Rb appears to be dispensable for normal cell cycling, but it has a special role in triggering permanent cell cycle exit associated with differentiation and senescence. Further, although the role of Rb as tumor suppressor is firmly established, it also has the ability to block apoptosis, which is generally thought to be a property of oncogenes. Our lab has been interested in understanding the dual and seemingly incongruous roles of Rb in cell cycle control and apoptosis. For many of these studies, we have chosen the melanocyte lineage as a model cell system because of the established role for Rb in melanocyte differentiation and survival, and the frequent deregulation of the Rb pathway in melanoma.

Animals↗

PubMed2005

Nitric oxide reductases of prokaryotes with emphasis on the respiratory, heme-copper oxidase type.

The investigation of respiratory N-oxide reduction as part of a biogeochemical process sustained by prokaryotes has roots over a century ago and has laid the groundwork for microbial nitric oxide (NO) biology and recognizing that NO is of bioenergetic importance as an electron acceptor in anaerobic environments. NO is an obligatory respiratory substrate of nitrate- and nitrite-denitrifying prokaryotes that release nitrous oxide or dinitrogen as products. We witness currently a broadening of the scope of NO functionality and an increase in awareness that other heme-based NO-metabolizing systems contribute to the overall capability of the prokaryotic cell to cope with NO both in anaerobic and aerobic environments, including the pathogen-host interface. NO reduction of newly recognized physiological importance is catalyzed by the pentaheme nitrite reductase, cytochrome c', flavohemoglobin and flavorubredoxin. Respiratory NO reductases are heme-nonheme Fe proteins that can be classified either in a short-chain group, which are complexes with cytochrome c, or a long-chain group, which have a fused quinol oxidase domain. Even though NORs are not proton pumps, both reductase groups are structural homologues of heme-copper oxidases. As a unique case, the short-chain NOR of Roseobacter denitrificans acts on oxygen, based on a heme b3-CuB center. In turn, certain heme-copper oxidases have significant turnover rates with NO. NOR mechanisms have been proposed from oxidase active site chemistry. Besides being a respiratory substrate, NO is also a signaling molecule that triggers gene expression of the principal components of NO respiration by members of the Crp-Fnr superfamily of transcription regulators.

Archaeal Proteins↗

PubMed2003

Evolutionary clues to DNA polymerase III beta clamp structural mechanisms.

The prokaryotic DNA polymerase III beta homodimeric clamp links the replication complex to DNA during polynucleotide synthesis. This clamp is loaded onto DNA and unloaded by the clamp loader complex, the delta subunit of which by itself can bind to and open the clamp. beta Clamps from diverse bacteria were examined using contrast hierarchical alignment and interaction network (CHAIN) analysis, a statistical approach that categorizes and measures the evolutionary constraints imposed on protein sequences by natural selection. Some constraints are subtle inasmuch as they are unique to certain bacteria. Examination of corresponding molecular interactions within structures of the Escherichia coli beta dimeric and delta-beta complexes reveals that N320, Y323 and R176, which are subject to very strong constraints, form a substructure that may serve as a platform for leveraging and directing delta-induced conformational changes. N320 may play a prominent role, as it is strategically situated between this substructure and regions linked to delta binding and opening of beta's dimeric interface. R176 appears to act as a relay between the delta binding site and the clamp's central hole. Other residues subject to strong constraints are likewise associated with structurally important features. For example, two pairs of interacting residues, R269/E304 and K74/E300, form salt bridges at the dimeric interface, while the C-terminal residues M362, P363, M364 and R365 appear to play key roles in delta binding. Q149 and K198 appear to sense DNA within the clamp's central hole while other residues may relay this information to the delta binding site. Mutagenesis experiments designed to explore possible mechanisms are proposed.

Amino Acid Sequence↗

PubMed2006

MODBASE: a database of annotated comparative protein structure models and associated resources.

MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (http://salilab.org/modweb). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, http://salilab.org/dbali), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, http://salilab.org/pibase) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, http://salilab.org/LS-SNP).

Binding Sites↗

PubMed2006

A rule-based emotion-dependent feature extraction method for emotion analysis from speech.

This paper presents a rule-based method to determine emotion-dependent features, which are defined from high-level features derived from the statistical measurements of prosodic parameters of speech. Emotion-dependent features are selected from high-level features using extraction rules. The ratio of emotional expression similarity between two speakers is defined by calculating the number and values of the emotion-dependent features that are present for the two speakers being compared. Emotional speech from Interface databases is used for evaluation of the proposed method, which was used to analyze emotional speech from five male and four female speakers in order to find any similarities and differences among individual speakers. The speakers are actors that have interpreted six emotions in four different languages. The results show that all the speakers share some universal signs regarding certain emotion-dependent features of emotional expression. Further analysis revealed that almost all speakers in the analysis used unique sets of emotion-dependent features and each speaker used unique values for the defined emotion-dependent features. The comparison among speakers shows that the expressed emotions can be analyzed according to two criteria. The first criterion is a defined set of emotion-dependent features and the second is an emotion-dependent feature value.

Adult↗