Proteolytic processing of the nonstructural proteins of dengue 2 virus

The genomes of many positive stranded RNA viruses and of all retroviruses are translated as large polyproteins which are proteolytically processed by cellular and viral proteases. Viral proteases are structurally related to two families of cellular proteases, the pepsin-like and trypsin-like proteases. This thesis describes the proteolytic processing of several nonstructural proteins of dengue 2 virus, a representative member of the Flaviviridae, and describes methods for transcribing full-length genomic RNA of dengue 2 virus. Chapter 1 describes the in vitro processing of the nonstructural proteins NS2A, NS2B and NS3. Chapter 2 describes a system that allows identification of residues within the protease that are directly or indirectly involved with substrate recognition. Chapter 3 describes methods to produce genome length dengue 2 RNA from cDNA templates.

The nonstructural protein NS3 is structurally related to viral trypsinlike proteases from the alpha-, picorna-, poty-, and pestiviruses. The hypothesis that the flavivirus nonstructural protein NS3 is a viral proteinase that generates the termini of several nonstructural proteins was tested using an efficient in vitro expression system and antisera specific for the nonstructural proteins NS2B and NS3. A series of cDNA constructs was transcribed using T7 RNA polymerase and the RNA translated in reticulocyte lysates. Proteolytic processing occurred in vitro to generate NS2B and NS3. The amino termini of NS2B and NS3 produced in vitro were found to be the same as the termini of NS2B and NS3 isolated from infected cells. Deletion analysis of cDNA constructs localized the protease domain necessary and sufficient for correct cleavage to the first 184 amino acids of NS3. Kinetic analysis of processing events in vitro and experiments to examine the sensitivity of processing to dilution suggested that an intramolecular cleavage between NS2A and NS2B preceded an intramolecular cleavage between NS2B and NS3. The data from these expression experiments confirm that NS3 is the viral proteinase responsible for cleavage events generating the amino termini of NS2B and NS3 and presumably for cleavages generating the termini of NS4A and NS5 as well.

Biochemical and genetic experiments using viral proteinases have defined the sequence requirements for cleavage site recognition, but have not identified residues within proteinases that interact with substrates. A biochemical assay was developed that could identify residues which were important for substrate recognition. Chimeric proteases between yellow fever and dengue 2 were constructed that allowed mapping of regions involved in substrate recognition, and site directed mutagenesis was used to modulate processing efficiency.

Expression in vitro revealed that the dengue protease domain efficiently processes the yellow fever polyprotein between NS2A and NS2B and between NS2B and NS3, but that the reciprocal construct is inactive. The dengue protease processes yellow fever cleavage sites more efficiently than dengue cleavage sites, suggesting that suboptimal cleavage efficiency may be used to increase levels of processing intermediates in vivo. By mutagenizing the putative substrate binding pocket it was possible to change the substrate specificity of the yellow fever protease; changing a minimum of three amino acids in the yellow fever protease enabled it to recognize dengue cleavage sites. This system allows identification of residues which are directly or indirectly involved with enzyme-substrate interaction, does not require a crystal structure, and can define the substrate preferences of individual members of a viral proteinase family.

Full-length cDNA clones, from which infectious RNA can be transcribed, have been developed for a number of positive strand RNA viruses, including the flavivirus type virus, yellow fever. The technology necessary to transcribe genomic RNA of dengue 2 virus was developed in order to better understand the molecular biology of the dengue subgroup. A 5' structural region clone was engineered to transcribe authentic dengue RNA that contains an additional 1 or 2 residues at the 5' end. A 3' nonstructural region clone was engineered to allow production of run off transcripts, and to allow directional ligation with the 5' structural region clone. In vitro ligation and transcription produces full-length genomic RNA which is noninfectious when transfected into mammalian tissue culture cells. Alternative methods for constructing cDNA clones and recovering live dengue virus are discussed.

Investigating the Role of the GET3-GET4/GET5 Interaction During Tail-Anchor Protein Targeting

The proper targeting of membrane proteins is essential to the viability of all cells. Tail-anchored (TA) proteins, defined as having a single transmembrane helix at their C-terminus, are post-translationally targeted to the endoplasmic reticulum (ER) membrane by the GET pathway (Guided Entry of TA proteins). In the yeast pathway, the handover of TA substrates is mediated by the heterotetrameric Get4/Get5 (Get4/5) complex, which tethers the co-chaperone Sgt2 to the central targeting factor, the Get3 ATPase. Although binding of Get4/5 to Get3 is critical for efficient TA targeting, the mechanisms by which Get4 regulates Get3 are unknown. To understand the molecular basis of Get4 function, we used a combination of structural biology, biochemistry, and cell biology. Get4/5 binds across the Get3 dimer interface, in an orientation only compatible with a closed Get3, providing insight into the role of nucleotide in complex formation. Additionally, this structure reveals two functionally distinct binding interfaces for anchoring and ATPase regulation, and loss of the regulatory interface leads to strong defects in vitro and in vivo. Additional crystal structures of the Get3-Get4/5 complex give rise to an alternate conformation, which represents an initial binding interaction mediated by electrostatics that facilitates the rate of subsequent inhibited complex formation. This interface is supported by an in-depth kinetic analysis of the Get3-Get4/5 interaction confirming the two-step complex formation. These results allow us to generate a refined model for Get4/5 function in TA targeting.

I. A study of the dynamics of triplet excitons in molecular crystals. II. An investigation of delayed light emission from Chlorella pyrenoidosa

I. PREAMBLE AND SCOPE

Brief introductory remarks, together with a definition of the scope of the material discussed in the thesis, are given.

II. A STUDY OF THE DYNAMICS OF TRIPLET EXCITONS IN MOLECULAR CRYSTALS

Phosphorescence spectra of pure crystalline naphthalene at room temperature and at 77˚ K are presented. The lifetime of the lowest triplet ³B_1u state of the crystal is determined from measurements of the time-dependence of the phosphorescence decay after termination of the excitation light. The fact that this lifetime is considerably shorter in the pure crystal at room temperature than in isotopic mixed crystals at 4.2˚ K is discussed, with special importance being attached to the mobility of triplet excitons in the pure crystal.

Excitation spectra of the delayed fluorescence and phosphorescence from crystalline naphthalene and anthracene are also presented. The equation governing the time- and spatial-dependence of the triplet exciton concentration in the crystal is discussed, along with several approximate equations obtained from the general equation under certain simplifying assumptions. The influence of triplet exciton diffusion on the observed excitation spectra and the possibility of using the latter to investigate the former is also considered. Calculations of the delayed fluorescence and phosphorescence excitation spectra of crystalline naphthalene are described.

A search for absorption of additional light quanta by triplet excitons in naphthalene and anthracene crystals failed to produce any evidence for the phenomenon. This apparent absence of triplet-triplet absorption in pure crystals is attributed to a low steady-state triplet concentration, due to processes like triplet-triplet annihilation, resulting in an absorption too weak to be detected with the apparatus used in the experiments. A comparison of triplet-triplet absorption by naphthalene in a glass at 77˚ K with that by naphthalene-h₈ in naphthalene-d₈ at 4.2˚ K is given. A broad absorption in the isotopic mixed crystal triplet-triplet spectrum has been tentatively interpreted in terms of coupling between the guest ³B_1u state and the conduction band and charge-transfer states of the host crystal.

III. AN INVESTIGATION OF DELAYED LIGHT EMISSION FROM Chlorella Pyrenoidosa

An apparatus capable of measuring emission lifetimes in the range 5 X 10^-9 sec to 6 X 10^-3 sec is described in detail. A cw argon ion laser beam, interrupted periodically by means of an electro-optic shutter, serves as the excitation source. Rapid sampling techniques coupled with signal averaging and digital data acquisition comprise the sensitive detection and readout portion of the apparatus. The capabilities of the equipment are adequately demonstrated by the results of a determination of the fluorescence lifetime of 5, 6, 11, 12-tetraphenyl-naphthacene in benzene solution at room temperature. Details of numerical methods used in the final data reduction are also described.

The results of preliminary measurements of delayed light emission from Chlorella Pyrenoidosa in the range 10^-3 sec to 1 sec are presented. Effects on the emission of an inhibitor and of variations in the excitation light intensity have been investigated. Kinetic analysis of the emission decay curves obtained under these various experimental conditions indicate that in the millisecond-to-second time interval the decay is adequately described by the sum of two first-order decay processes. The values of the time constants of these processes appear to be sensitive both to added inhibitor and to excitation light intensity.

Nanocomposites de Poliuretanos Elastoméricos y Nanotubos de Carbono Multipared

218p. -- Tesis con mención "Doctor europeus" realizada en el periodo de Octubre 2005-Mayo 2010, en el Grupo "Materiales+Tecnologías" (GMT).

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

Effect of swelling response of the support particles on ethylene polymerization

Macroporous and modified macroporous poly(styrene-co-methyl methacrylate-co-divinylbenzene) particles (m-PS and mm-PS) supported Cp2ZrCl2 were prepared and applied to ethylene polymerization using methylaluminoxane (MAO) as cocatalyst. The influences of the swelling response of the support particles on the catalyst loading capabilities of the supports as well as on the activities of the supported catalysts were studied. It was shown that the Zr loadings of the supports and the activities of the supported catalysts increased with the swelling extent of the support particles. The m-PS or mm-PS supported catalysts exhibited very high activities when the support particles were well swollen, whereas those catalysts devoid of swelling treatment gave much lower activities. Investigation on the distribution of the supports in the polyethylene by TEM indicated that the swelling of the support particles allowed the fragmentation of the catalyst particles. In contrast, the fragmentation of the support particles with poor swelling was hindered during ethylene polymerization.

Synthesis of asymmetric H-shaped block copolymer by the combination of atom transfer radical polymerization and living anionic polymerization

A new asymmetric H-shaped block copolymer (PS)(2)-PEO-(PMMA)(2) has been designed and successfully synthesized by the combination of atom transfer radical polymerization and living anionic polymerization. The synthesized 2,2-dichloro acetate-ethylene glycol (DCAG) was used to initiate the polymerization of styrene by ATRP to yield a symmetric homopolymer (Cl-PS)(2)-CHCCCCH2CH2OH with an active hydroxyl group. The chlorine was removed to yield the (PS)(2)-CHCOOCH2CH2OH ((PS)(2)-OH). The hydroxyl group of the (PS)(2)-OH, which is an active species of the living anionic polymerization, was used to initiate ethylene oxide by living anionic polymerization via DPMK to yield (PS)(2)-PEO-OH. The (PS)(2)-PEO-OH was reacted with the 2,2-dichloro acetyl chloride to yield (PS)(2)-PEO-OCCHCl2 ((PS)(2)-PEO-DCA). The asymmetric H-shaped block polymer (PS)(2)-PEO-(PMMA)(2) was prepared via ATRP of MMA at 130 degrees C using (PS)(2)-PEO-DCA as initiator and CuCl/bPy as the catalyst system. The architectures of the asymmetric H-shaped block copolymers, (PS)(2)-PEO-(PMMA)(2), were confirmed by H-1 NMR, GPC and Fr-IR.

Cobalt(II)hexacyanoferrate film modified glassy carbon electrode for construction of a glucose biosensor

An amperometric glucose biosensor was constructed based on a glassy carbon electrode modified with a Cobalt(II)hexacyanoferrate film which catalyzes electroreduction of hydrogen peroxide. Gelatin was used as immobilization matrix. Interference could be effectively eliminated by the combination of low detection potential with a Nafion coating. A low applied potential can avoid oxidation of interferences such as ascorbic acid, uric acid, p-acetyl-aminophenol, etc.. Nafion coating prevents interferences from access to the electrode surface by electrostatic repulsion. A wide linear range of detection was obtained. Analytical performance parameters are given and kinetic analysis discussed.

Crystallization kinetics of poly(ether ether ketone) (PEEK) from its metastable melt

After isothermal crystallization of the amorphous poly(ether ether ketone), double endothermic behaviour can be found through differential scanning calorimetry experiments. During the heating scan of semicrystalline PEEK, a metastable melt, which comes from the melt of the thinner lamellar crystal populations, can be obtained between these two endotherms. The metastable melt can recrystallize immediately just above the lower melting temperature and form slightly thicker lamellae than the original ones. The thickness and the perfection depend upon the crystallization time and the crystallization temperature. By comparing the TEM morphological observations of the samples before and after partial melting, it can be shown that lamellar crystals, having different thermodynamic stability, form during isothermal crystallization. After partial melting, only the type of lamellar crystal exhibiting the higher thermodynamic stability remains. Wide angle X-ray diffraction measurements shows a slightly change in the crystallinity of the samples before and after the partial melting. Small angle X-ray scattering results exhibit a change in the long period of the lamellar crystals before and after the partial melting process. The crystallization kinetics of the metastable melt can be determined by means of differential scanning calorimetry. The kinetic analysis showed that the isothermal crystallization of the metastable PEEK melt proceeds with an Avrami exponent of n = 1.0 similar to 1.4, reflecting that probably one-dimensional or an irregular line growth of the crystal occurred between the existing main lamellae with heterogeneous nucleation. (C) 1998 Elsevier Science Ltd. All rights reserved.

Isothermal crystallization studies on neodymium oxide filled nylon 6

Melt mixing of nylon 8 with neodymium oxide particles was carried out with a single-screw extruder. The crystal behaviors of plain nylon 6 and the neodymium oxide filled nylon 6 mixture were studied by means of isothermal crystallization kinetic analysis. Isothermal crystallization thermograms obtained by differential scanning calorimetry (DSC) were analyzed based on the Avrami equation. The neodymium oxide particles acted as a nucleating agent in the mixture. The overall rate of di-isothermal crystallization of the neodymium oxide filled nylon 6 mixture is higher than that of plain nylon 6. The mechanism and modes of plain nylon 6 were the same as those of neodymium oxide filled PA6 mixture.

CO multipulse TAP studies of 2% Pt/CeO2 catalyst: Influence of catalyst pretreatment and temperature on the number of active sites observed

CO multipulse temporal analysis of products (TAP) experiments were used to characterize a ceria-supported platinum catalyst after various oxidative and reductive pretreatments using O-2, H2O, CO2, and H-2. Based on the amount of CO consumed, using the final CO-saturated catalyst composition as the common state point, the oxidatively pretreated catalyst could be described using a general scale. From a kinetic analysis of the CO multipulse responses, two kinetic regimes corresponding to two types of active sites could be identified. As the temperature was raised, the number of the most active sites did not change while the amount of the less active site increased. Comparison of the number of active sites determined from the TAP data reported herein with that determined by a previous steady-state isotope transient kinetic analysis experiment showed excellent agreement. This correlation indicates that the (very fast response) TAP experiments can provide information regarding the number and type of active sites that are relevant to a catalyst under real reaction conditions. (c) 2007 Elsevier Inc. All rights reserved.

On the complexity of the water-gas shift reaction mechanism over a Pt/CeO2 catalyst: Effect of the temperature on the reactivity of formate surface species studied by operando DRIFT during isotopic transient at chemical steady-state

The present report investigates the role of formate species as potential reaction intermediates for the WGS reaction (CO + H2O -> CO2 + H-2) over a Pt-CeO2 catalyst. A combination of operando techniques, i.e., in situ diffuse reflectance FT-IR (DRIFT) spectroscopy and mass spectrometry (MS) during steady-state isotopic transient kinetic analysis (SSITKA), was used to relate the exchange of the reaction product CO2 to that of surface formate species. The data presented here suggest that a switchover from a non-formate to a formate-based mechanism could take place over a very narrow temperature range (as low as 60 K) over our Pt-CeO2 catalyst. This observation clearly stresses the need to avoid extrapolating conclusions to the case of results obtained under even slightly different experimental conditions. The occurrence of a low-temperature mechanism, possibly redox or Mars van Krevelen-like, that deactivates above 473 K because of ceria over-reduction is suggested as a possible explanation for the switchover, similarly to the case of the CO-NO reaction over Cu, I'd and Rh-CeZrOx (see Kaspar and co-workers [1-3]). (c) 2006 Elsevier B.V. All rights reserved.