971 resultados para Protein-polymer Virial Coefficients


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Membrane proteins play an indispensable role in physiological processes. It is, therefore, not surprising that many diseases are based on the malfunction of membrane proteins. Hence membrane proteins and especially G-protein coupled receptors(GPCRs)- the largest subfamily- have become an important drug target. Due to their high selectivity and sensitivity membrane proteins are also feasible for the detection of small quantities of substances with biosensors. Despite this widespread interest in GPCRs due to their importance as drug targets and biosensors there is still a lack of knowledge of structure, function and endogenous ligands for quiet a few of the previously identified receptors.rnBottlenecks in over-expression, purification, reconstitution and handling of membrane proteins arise due to their hydrophobic nature. Therefore the production of reasonable amounts of functional membrane proteins for structural and functional studies is still challenging. Also the limited stability of lipid based membrane systems hampers their application as platforms forrnscreening applications and biosensors.rnIn recent years the in vitro protein synthesis became a promising alternative to gain better yields for expression of membrane proteins in bio-mimetic membrane systems. These expression systems are based on cell extracts. Therefore cellular effects on protein expression are reduced. The open nature of the cell-free expression systems easily allows for the adjustment of reactionrnconditions for the protein of interest. The cell-free expression in the presence of bio-mimetic membrane systems allows the direct incorporation of the membrane proteins and therefore skips the time-consuming purification and reconstitution processes. Amphiphilic block-copolymers emerged as promising alternative for the less stable lipid-based membrane systems. They, likernlipids, form membraneous structures in aqueous solutions but exhibit increased mechanical and chemical stability.rnThe aim of this work was the generation of a GPCR-functionalised membrane system by combining both promising alternatives: in vitro synthesis and polymeric membrane systems. This novel platform should be feasible for the characterisation of the incorporated GPCR. Immunodetection of Dopamine receptor 1 and 2 expressed in diblock- and triblock-polymersomes demonstrated the successful in vitro expression of GPCRs in polymeric membranes. Antibodyrnbinding studies suggested a favoured orientation of dopamine receptors in triblockpolymersomes.rnA dopamine-replacement assay on DRD2-functionalised immobilised triblockpolymersomes confirmed functionality of the receptor in the polymersomes. The altered binding curve suggests an effect of the altered hydrophobic environment presented by the polymer membrane on protein activity.

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Ziel der vorliegenden Dissertation war es, Einblicke in das Kristallisationsverhalten weicher Materie („soft matter“), wie verschiedener Polymere oder Wasser, unter räumlicher Einschränkung („confinement“) zu erlangen. Dabei sollte untersucht werden, wie, weshalb und wann die Kristallisation in nanoporösen Strukturen eintritt. Desweiteren ist Kristallisation weicher Materie in nanoporösen Strukturen nicht nur aus Aspekten der Grundlagenforschung von großem Interesse, sondern es ergeben sich zahlreiche praktische Anwendungen. Durch die gezielte Steuerung der Kristallinität von Polymeren könnten somit Materialien mit verschiendenen mechanischen und optischen Eigenschaften erhalten werden. Desweiteren wurde auch räumlich eingeschränktes Wasser untersucht. Dieses spielt eine wichtige Rolle in der Molekularbiologie, z.B. für das globuläre Protein, und als Wolkenkondensationskeime in der Atmosphärenchemie und Physik. Auch im interstellaren Raum ist eingeschränktes Wasser in Form von Eispartikeln anzutreffen. Die Kristallisation von eingeschränktem Wasser zu verstehen und zu beeinflussen ist letztlich auch für die Haltbarkeit von Baumaterialien wie etwa Zement von großem Interesse.rnUm dies zu untersuchen wird Wasser in der Regel stark abgekühlt und das Kristallisationsverhalten in Abhängigkeit des Volumens untersucht. Dabei wurde beobachtet, dass Mikro- bzw. Nanometer große Volumina erst ab -38 °C bzw. -70 °C kristallisieren. Wasser unterliegt dabei in der Regel dem Prozess der homogenen Nukleation. In der Regel gefriert Wasser aber bei höheren Temperaturen, da durch Verunreinigungen eine vorzeitige, heterogene Nukleation eintritt.rnDie vorliegende Arbeit untersucht die sachdienlichen Phasendiagramme von kristallisierbaren Polymeren und Wasser unter räumlich eingeschränkten Bedingungen. Selbst ausgerichtetes Aluminiumoxid (AAO) mit Porengrößen im Bereich von 25 bis 400 nm wurden als räumliche Einschränkung sowohl für Polymere als auch für Wasser gewählt. Die AAO Nanoporen sind zylindrisch und parallel ausgerichtet. Außerdem besitzen sie eine gleichmäßige Porenlänge und einen gleichmäßigen Durchmesser. Daher eignen sie sich als Modelsystem um Kristallisationsprozesse unter wohldefinierter räumlicher Einschränkung zu untersuchen.rnEs wurden verschiedene halbkristalline Polymere verwendet, darunter Poly(ethylenoxid), Poly(ɛ-Caprolacton) und Diblockcopolymere aus PEO-b-PCL. Der Einfluss der Porengröße auf die Nukleation wurde aus verschiedenen Gesichtspunkten untersucht: (i) Einfluss auf den Nukleationmechanismus (heterogene gegenüber homogener Nukleation), (ii) Kristallorientierung und Kristallinitätsgrad und (iii) Zusammenhang zwischen Kristallisationstemperatur bei homogener Kristallisation und Glasübergangstemperatur.rnEs konnte gezeigt werden, dass die Kristallisation von Polymeren in Bulk durch heterogene Nukleation induziert wird und das die Kristallisation in kleinen Poren hauptsächlich über homogene Nukleation mit reduzierter und einstellbarer Kristallinität verläuft und eine hohe Kristallorientierung aufweist. Durch die AAOs konnte außerdem die kritische Keimgröße für die Kristallisation der Polymere abgeschätzt werden. Schließlich wurde der Einfluss der Polydispersität, von Oligomeren und anderen Zusatzstoffen auf den Nukleationsmechanismus untersucht.rn4rnDie Nukleation von Eis wurde in den selben AAOs untersucht und ein direkter Zusammenhang zwischen dem Nukleationstyp (heterogen bzw. homogen) und der gebildeten Eisphase konnte beobachtet werden. In größeren Poren verlief die Nukleation heterogen, wohingegen sie in kleineren Poren homogen verlief. Außerdem wurde eine Phasenumwandlung des Eises beobachtet. In den größeren Poren wurde hexagonales Eis nachgewiesen und unter einer Porengröße von 35 nm trat hauptsächlich kubisches Eis auf. Nennenswerter Weise handelte es sich bei dem kubischem Eis nicht um eine metastabile sondern eine stabile Phase. Abschließend wird ein Phasendiagramm für räumlich eingeschränktes Wasser vorgeschlagen. Dieses Phasendiagramm kann für technische Anwendungen von Bedeutung sein, so z.B. für Baumaterial wie Zement. Als weiteres Beispiel könnten AAOs, die die heterogene Nukleation unterdrücken (Porendurchmesser ≤ 35 nm) als Filter für Reinstwasser zum Einsatz kommen.rnNun zur Anfangs gestellten Frage: Wie unterschiedlich sind Wasser und Polymerkristallisation voneinander unter räumlicher Einschränkung? Durch Vergleich der beiden Phasendiagramme kommen wir zu dem Schluss, dass beide nicht fundamental verschieden sind. Dies ist zunächst verwunderlich, da Wasser ein kleines Molekül ist und wesentlich kleiner als die kleinste Porengröße ist. Wasser verfügt allerdings über starke Wasserstoffbrückenbindungen und verhält sich daher wie ein Polymer. Daher auch der Name „Polywasser“.

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Polymers that are used in clinical practice as bone-defect-filling materials possess many essential qualities, such as moldability, mechanical strength and biodegradability, but they are neither osteoconductive nor osteoinductive. Osteoconductivity can be conferred by coating the material with a layer of calcium phosphate, which can be rendered osteoinductive by functionalizing it with an osteogenic agent. We wished to ascertain whether the morphological and physicochemical characteristics of unfunctionalized and bovine-serum-albumin (BSA)-functionalized calcium-phosphate coatings were influenced by the surface properties of polymeric carriers. The release kinetics of the protein were also investigated. Two sponge-like materials (Helistat® and Polyactive®) and two fibrous ones (Ethisorb and poly[lactic-co-glycolic acid]) were tested. The coating characteristics were evaluated using state-of-the-art methodologies. The release kinetics of BSA were monitored spectrophotometrically. The characteristics of the amorphous and the crystalline phases of the coatings were not influenced by either the surface chemistry or the surface geometry of the underlying polymer. The mechanism whereby BSA was incorporated into the crystalline layer and the rate of release of the truly incorporated depot were likewise unaffected by the nature of the polymeric carrier. Our biomimetic coating technique could be applied to either spongy or fibrous bone-defect-filling organic polymers, with a view to rendering them osteoconductive and osteoinductive.

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Binding of hydrophobic chemicals to colloids such as proteins or lipids is difficult to measure using classical microdialysis methods due to low aqueous concentrations, adsorption to dialysis membranes and test vessels, and slow kinetics of equilibration. Here, we employed a three-phase partitioning system where silicone (polydimethylsiloxane, PDMS) serves as a third phase to determine partitioning between water and colloids and acts at the same time as a dosing device for hydrophobic chemicals. The applicability of this method was demonstrated with bovine serum albumin (BSA). Measured binding constants (K(BSAw)) for chlorpyrifos, methoxychlor, nonylphenol, and pyrene were in good agreement with an established quantitative structure-activity relationship (QSAR). A fifth compound, fluoxypyr-methyl-heptyl ester, was excluded from the analysis because of apparent abiotic degradation. The PDMS depletion method was then used to determine partition coefficients for test chemicals in rainbow trout (Oncorhynchus mykiss) liver S9 fractions (K(S9w)) and blood plasma (K(bloodw)). Measured K(S9w) and K(bloodw) values were consistent with predictions obtained using a mass-balance model that employs the octanol-water partition coefficient (K(ow)) as a surrogate for lipid partitioning and K(BSAw) to represent protein binding. For each compound, K(bloodw) was substantially greater than K(S9w), primarily because blood contains more lipid than liver S9 fractions (1.84% of wet weight vs 0.051%). Measured liver S9 and blood plasma binding parameters were subsequently implemented in an in vitro to in vivo extrapolation model to link the in vitro liver S9 metabolic degradation assay to in vivo metabolism in fish. Apparent volumes of distribution (V(d)) calculated from the experimental data were similar to literature estimates. However, the calculated binding ratios (f(u)) used to relate in vitro metabolic clearance to clearance by the intact liver were 10 to 100 times lower than values used in previous modeling efforts. Bioconcentration factors (BCF) predicted using the experimental binding data were substantially higher than the predicted values obtained in earlier studies and correlated poorly with measured BCF values in fish. One possible explanation for this finding is that chemicals bound to proteins can desorb rapidly and thus contribute to metabolic turnover of the chemicals. This hypothesis remains to be investigated in future studies, ideally with chemicals of higher hydrophobicity.

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With recent advances in mass spectrometry techniques, it is now possible to investigate proteins over a wide range of molecular weights in small biological specimens. This advance has generated data-analytic challenges in proteomics, similar to those created by microarray technologies in genetics, namely, discovery of "signature" protein profiles specific to each pathologic state (e.g., normal vs. cancer) or differential profiles between experimental conditions (e.g., treated by a drug of interest vs. untreated) from high-dimensional data. We propose a data analytic strategy for discovering protein biomarkers based on such high-dimensional mass-spectrometry data. A real biomarker-discovery project on prostate cancer is taken as a concrete example throughout the paper: the project aims to identify proteins in serum that distinguish cancer, benign hyperplasia, and normal states of prostate using the Surface Enhanced Laser Desorption/Ionization (SELDI) technology, a recently developed mass spectrometry technique. Our data analytic strategy takes properties of the SELDI mass-spectrometer into account: the SELDI output of a specimen contains about 48,000 (x, y) points where x is the protein mass divided by the number of charges introduced by ionization and y is the protein intensity of the corresponding mass per charge value, x, in that specimen. Given high coefficients of variation and other characteristics of protein intensity measures (y values), we reduce the measures of protein intensities to a set of binary variables that indicate peaks in the y-axis direction in the nearest neighborhoods of each mass per charge point in the x-axis direction. We then account for a shifting (measurement error) problem of the x-axis in SELDI output. After these pre-analysis processing of data, we combine the binary predictors to generate classification rules for cancer, benign hyperplasia, and normal states of prostate. Our approach is to apply the boosting algorithm to select binary predictors and construct a summary classifier. We empirically evaluate sensitivity and specificity of the resulting summary classifiers with a test dataset that is independent from the training dataset used to construct the summary classifiers. The proposed method performed nearly perfectly in distinguishing cancer and benign hyperplasia from normal. In the classification of cancer vs. benign hyperplasia, however, an appreciable proportion of the benign specimens were classified incorrectly as cancer. We discuss practical issues associated with our proposed approach to the analysis of SELDI output and its application in cancer biomarker discovery.

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EPON 862 is an epoxy resin which is cured with the hardening agent DETDA to form a crosslinked epoxy polymer and is used as a component in modern aircraft structures. These crosslinked polymers are often exposed to prolonged periods of temperatures below glass transition range which cause physical aging to occur. Because physical aging can compromise the performance of epoxies and their composites and because experimental techniques cannot provide all of the necessary physical insight that is needed to fully understand physical aging, efficient computational approaches to predict the effects of physical aging on thermo-mechanical properties are needed. In this study, Molecular Dynamics and Molecular Minimization simulations are being used to establish well-equilibrated, validated molecular models of the EPON 862-DETDA epoxy system with a range of crosslink densities using a united-atom force field. These simulations are subsequently used to predict the glass transition temperature, thermal expansion coefficients, and elastic properties of each of the crosslinked systems for validation of the modeling techniques. The results indicate that glass transition temperature and elastic properties increase with increasing levels of crosslink density and the thermal expansion coefficient decreases with crosslink density, both above and below the glass transition temperature. The results also indicate that there may be an upper limit to crosslink density that can be realistically achieved in epoxy systems. After evaluation of the thermo-mechanical properties, a method is developed to efficiently establish molecular models of epoxy resins that represent the corresponding real molecular structure at specific aging times. Although this approach does not model the physical aging process, it is useful in establishing a molecular model that resembles the physically-aged state for further use in predicting thermo-mechanical properties as a function of aging time. An equation has been predicted based on the results which directly correlate aging time to aged volume of the molecular model. This equation can be helpful for modelers who want to study properties of epoxy resins at different levels of aging but have little information about volume shrinkage occurring during physical aging.

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Chromatin, composed of repeating nucleosome units, is the genetic polymer of life. To aid in DNA compaction and organized storage, the double helix wraps around a core complex of histone proteins to form the nucleosome, and is therefore no longer freely accessible to cellular proteins for the processes of transcription, replication and DNA repair. Over the course of evolution, DNA-based applications have developed routes to access DNA bound up in chromatin, and further, have actually utilized the chromatin structure to create another level of complexity and information storage. The histone molecules that DNA surrounds have free-floating tails that extend out of the nucleosome. These tails are post-translationally modified to create docking sites for the proteins involved in transcription, replication and repair, thus providing one prominent way that specific genomic sequences are accessed and manipulated. Adding another degree of information storage, histone tail-modifications paint the genome in precise manners to influence a state of transcriptional activity or repression, to generate euchromatin, containing gene-dense regions, or heterochromatin, containing repeat sequences and low-density gene regions. The work presented here is the study of histone tail modifications, how they are written and how they are read, divided into two projects. Both begin with protein microarray experiments where we discover the protein domains that can bind modified histone tails, and how multiple tail modifications can influence this binding. Project one then looks deeper into the enzymes that lay down the tail modifications. Specifically, we studied histone-tail arginine methylation by PRMT6. We found that methylation of a specific histone residue by PRMT6, arginine 2 of H3, can antagonize the binding of protein domains to the H3 tail and therefore affect transcription of genes regulated by the H3-tail binding proteins. Project two focuses on a protein we identified to bind modified histone tails, PHF20, and was an endeavor to discover the biological role of this protein. Thus, in total, we are looking at a complete process: (1) histone tail modification by an enzyme (here, PRMT6), (2) how this and other modifications are bound by conserved protein domains, and (3) by using PHF20 as an example, the functional outcome of binding through investigating the biological role of a chromatin reader. ^

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The solubility parameters of two SBS commercial rubbers with different structures (lineal and radial), and with slightly different styrene content have been determined by inverse gas chromatography technique. The Flory–Huggins interaction parameters of several polymer–solvent mixtures have also been calculated. The influence of the polymer composition, the solvent molecular weight and the temperature over these parameters have been discussed; besides, these parameters have been compared with previous ones, obtained by intrinsic viscosity measurements. From the Flory–Huggins interaction parameters, the infinite dilution activity coefficients of the solvents have been calculated and fitted to the well-known NRTL model. These NRTL binary interaction parameters have a great importance in modelling the separation steps in the process of obtaining the rubber.

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Thermomechanical relaxation events and different water states in cottonseed protein bioplastics are presented whilst investigating the effects of aldehyde cross-linking agents. Thermomechanical relaxation of cottonseed protein bioplastics associated with protein denaturation, moisture absorption and broad glass transitions (Tg) were observed from DSC and DMA measurements. It was shown that variation of the aldehyde influences the storage modulus at very low temperature (below Tg). From measurements of the water fusion point, enthalpy, vaporisation, and weight loss, three water states in the water-absorbed bioplastics are suggested; namely strongly-bound-to-polymer, weakly-bound-to-polymer and bulk-like water. The water content and unreacted cross-linking agents are influential factors in controlling formation of the different water states, whilst the selection of different aldehydes was found to be negligible. These results could be valuable for adjusting the thermomechanical relaxations of protein based bioplastics, and tailoring their properties in wet environments.

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The fluorescence of a polyanionic conjugated polymer can be quenched by extremely low concentrations of cationic electron acceptors in aqueous solutions. We report a greater than million-fold amplification of the sensitivity to fluorescence quenching compared with corresponding “molecular excited states.” Using a combination of steady-state and ultrafast spectroscopy, we have established that the dramatic quenching results from weak complex formation [polymer(−)/quencher(+)], followed by ultrafast electron transfer from excitations on the entire polymer chain to the quencher, with a time constant of 650 fs. Because of the weak complex formation, the quenching can be selectively reversed by using a quencher-recognition diad. We have constructed such a diad and demonstrate that the fluorescence is fully recovered on binding between the recognition site and a specific analyte protein. In both solutions and thin films, this reversible fluorescence quenching provides the basis for a new class of highly sensitive biological and chemical sensors.

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Both high- and low-molecular-weight glutenin subunits (LMW-GS) play the major role in determining the viscoelastic properties of wheat (Triticum aestivum L.) flour. To date there has been no clear correspondence between the amino acid sequences of LMW-GS derived from DNA sequencing and those of actual LMW-GS present in the endosperm. We have characterized a particular LMW-GS from hexaploid bread wheat, a major component of the glutenin polymer, which we call the 42K LMW-GS, and have isolated and sequenced the putative corresponding gene. Extensive amino acid sequences obtained directly for this 42K LMW-GS indicate correspondence between this protein and the putative corresponding gene. This subunit did not show a cysteine (Cys) at position 5, in contrast to what has frequently been reported for nucleotide-based sequences of LMW-GS. This Cys has been replaced by one occurring in the repeated-sequence domain, leaving the total number of Cys residues in the molecule the same as in various other LMW-GS. On the basis of the deduced amino acid sequence and literature-based assignment of disulfide linkages, a computer-generated molecular model of the 42K subunit was constructed.

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A capillary electrophoresis method has been developed to study DNA-protein complexes by mobility-shift assay. This method is at least 100 times more sensitive than conventional gel mobility-shift procedures. Key features of the technique include the use of a neutral coated capillary, a small amount of linear polymer in the separation medium, and use of covalently dye-labeled DNA probes that can be detected with a commercially available laser-induced fluorescence monitor. The capillary method provides quantitative data in runs requiring < 20 min, from which dissociation constants are readily determined. As a test case we studied interactions of a developmentally important sea urchin embryo transcription factor, SpP3A2. As little as 2-10 x 10(6) molecules of specific SpP3A2-oligonucleotide complex were reproducibly detected, using recombinant SpP3A2, crude nuclear extract, egg lysates, and even a single sea urchin egg lysed within the capillary column.

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Autonomously replicating sequence (ARS) elements of the fission yeast Schizosaccharomyces pombe contain multiple imperfect copies of the consensus sequence reported by Maundrell et al. [Maundrell K., Hutchison, A. & Shall, S. (1988) EMBO J. 7, 2203-2209]. When cell free extracts of S. pombe were incubated with a dimer or tetramer of an oligonucleotide containing the ARS consensus sequence, several complexes were detected using a gel mobility-shift assay. The proteins forming these complexes also bind ars3002, which is the most active origin in the ura4 region of chromosome III of S. pombe. One protein, partly responsible for the binding activity observed with crude extracts, was purified to near homogeneity. It is a 60-kDa protein and was named ARS-binding protein 1 (Abp1). Abp1 preferentially binds to multiple sites in ARS 3002 and to the DNA polymer poly[d(A.T)]. The cloning and sequence of the gene coding for Abp1 revealed that it encodes a protein of 59.8 kDa (522 amino acids). Abp1 has significant homology (25% identity, 50% similarity) to the N-terminal region (approximately 300 amino acids) of the human and mouse centromere DNA-binding protein CENP-B. Because centromeres of S. pombe contain a high density of ARS elements, Abp1 may play a role connecting DNA replication and chromosome segregation.

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The bacterial cell division protein FtsZ is a homolog of tubulin, but it has not been determined whether FtsZ polymers are structurally related to the microtubule lattice. In the present study, we have obtained high-resolution electron micrographs of two FtsZ polymers that show remarkable similarity to tubulin polymers. The first is a two-dimensional sheet of protofilaments with a lattice very similar to that of the microtubule wall. The second is a miniring, consisting of a single protofilament in a sharply curved, planar conformation. FtsZ minirings are very similar to tubulin rings that are formed upon disassembly of microtubules but are about half the diameter. This suggests that the curved conformation occurs at every FtsZ subunit, but in tubulin rings the conformation occurs at either beta- or alpha-tubulin subunits but not both. We conclude that the functional polymer of FtsZ in bacterial cell division is a long thin sheet of protofilaments. There is sufficient FtsZ in Escherichia coli to form a protofilament that encircles the cell 20 times. The similarity of polymers formed by FtsZ and tubulin implies that the protofilament sheet is an ancient cytoskeletal system, originally functioning in bacterial cell division and later modified to make microtubules.

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The relationship between spot volume and variation for all protein spots observed on large format 2D gels when utilising silver stain technology and a model system based on mammalian NSO cell extracts is reported. By running multiple gels we have shown that the reproducibility of data generated in this way is dependent on individual protein spot volumes, which in turn are directly correlated with the coefficient of variation. The coefficients of variation across all observed protein spots were highest for low abundant proteins which are the primary contributors to process error, and lowest for more abundant proteins. Using the relationship between spot volume and coefficient of variation we show it is necessary to calculate variation for individual protein spot volumes. The inherent limitations of silver staining therefore mean that errors in individual protein spot volumes must be considered when assessing significant changes in protein spot volume and not global error. (C) 2003 Elsevier Science (USA). All rights reserved.