A novel activation mechanism for Clostridial bacteriophage endolysins

Bacteriophage-encoded endolysins are produced at the end of the phage lytic cycle for the degradation of the host bacterial cell. Endolysins offer the potential as alternatives to antibiotics as biocontrol agents or therapeutics. The lytic mechanisms of three bacteriophage endolysins that target Clostridium species living under different conditions were investigated. For these endolysins a trigger and release mechanism is proposed for their activation. During host lysis, holin lesion formation suddenly permeabilises the membrane which exposes the cytosol-sequestered endolysins to a sudden environmental shock. This shock is suggested to trigger a conformational switch of the endolysins between two distinct dimer states. The switch between dimer states is proposed to activate a novel autocleavage mechanism that cleaves the linker connecting the N-terminal catalytic domain and the C-terminal domain to release the catalytic domain for more efficient digestion of the bacterial cell wall. Crystal structures of cleaved fragments of CD27L and CTP1L were previously obtained. In these structures cleavage occurs at the stem of the linker connected to the C-terminal domain. Despite a sequence identity of only 22% between 81 residues of the C-terminal domains of CD27L and CTP1L, they represent a novel fold that is identified in a number of different lysins. Within the crystal structures the two distinct dimerization modes are represented: the elongated head‐on dimer and the side-by‐side dimer. Introducing mutations that inhibit either of the dimerization states caused a decrease in the efficiency of both the autocleavage mechanism and the lytic activity of the endolysins. The two dimer states were validated for the full-length endolysins in solution by using right angle light scattering, small angle X‐ray scattering and cross-linking experiments. Overall, the data represents a new type of regulation governed by the C-terminal domains that is used to activate these endolysins once they enter the bacterial cell wall.

THERMODYNMICS AND STRUCTURE OF POLY(ETHYLENE OXIDE) IN MIXTURES OF WATER AND ETHANOL

Poly(ethylene oxide) (PEO) is one of the most researched synthetic polymers due to the complex behavior which arises from the interplay of the hydrophilic and hydrophobic sites on the polymer chain. PEO in ethanol forms an opaque gel-like mixture with a partially crystalline structure. Addition of a small amount of water disrupts the gel: 5 wt % PEO in ethanol becomes a transparent solution with the addition of 4 vol % water. The phase behavior of PEO in mixed solvents have been studied using small-angle neutron scattering (SANS). PEO solutions (5 wt % PEO) which contain 4 vol % - 10 vol % (and higher) water behave as an athermal polymer solution and the phase behavior changes from UCST to LCST rapidly as the fraction of water is increased. 2 wt % PEO in water and 10 wt % PEO in ethanol/ water mixtures are examined to assess the role of hydration. The observed phase behavior is consistent with a hydration layer forming upon the addition of water as the system shifts from UCST to LCST behavior. At the molecular level, two or three water molecules can hydrate one PEO monomer (water molecules form a sheath around the PEO macromolecule) which is consistent with the suppression of crystallization and change in the mentioned phase behavior as observed by SANS. The clustering effect of aqueous PEO solution (M.W of PEO = 90,000 g/mol) is monitored as an excess scattering intensity at low-Q. Clustering intensity at Q = 0.004 Å^-1 is used for evaluating the clustering effect. The clustering intensity is proportional to the inverse temperature and levels off when the temperature is less than 50 ˚C. When the temperature is increased over 50 ˚C, the clustering intensity starts decreasing. The clustering of PEO is monitored in ethanol/ water mixtures. The clustering intensity increases as the fraction of water is increased. Based on the solvation intensity behavior, we confirmed that the ethanol/ water mixtures obey a random solvent mixing rule, whereby solvent mixtures are better at solvating the polymer that any of the two solvents. The solution behavior of PEO in ethanol was investigated in the presence of salt (CaCl2) using SANS. Binding of Ca2+ ions to the PEO oxygens transforms the neutral polymer to a weakly charged polyelectrolyte. We observed that the PEO/ethanol solution is better solvated at higher salt concentration due to the electrostatic repulsion of weakly charged monomers. The association of the Ca2+ ions with the PEO oxygen atoms transforms the neutral polymer to a weakly charged polyelectrolyte and gives rise to repulsive interactions between the PEO/Ca2+ complexes. Addition of salt disrupts the gel, which is consistent with better solvation as the salt concentration is increased. Moreover, SANS shows that the phase behavior of PEO/ethanol changes from UCST to LCST as the salt concentration is increased.

Solution structure of the N-terminal transactivation domain of ERM modified by SUMO-1.

ERM is a member of the PEA3 group of the Ets transcription factor family that plays important roles in development and tumorigenesis. The PEA3s share an N-terminal transactivation domain (TADn) whose activity is inhibited by small ubiquitin-like modifier (SUMO). However, the consequences of sumoylation and its underlying molecular mechanism remain unclear. The domain structure of ERM TADn alone or modified by SUMO-1 was analyzed using small-angle X-ray scattering (SAXS). Low resolution shapes determined ab initio from the scattering data indicated an elongated shape and an unstructured conformation of TADn in solution. Covalent attachment of SUMO-1 does not perturb the structure of TADn as indicated by the linear arrangement of the SUMO moiety with respect to TADn. Thus, ERM belongs to the growing family of proteins that contain intrinsically unstructured regions. The flexible nature of TADn may be instrumental for ERM recognition and binding to diverse molecular partners.

Determination of micelle/water partition coefficients and associated thermodynamic data for dialkyl phthalate esters

Micelle/water partition coefficients for three dialkyl phthalate esters - dimethyl phthalate ester (DMP), diethyl phthalate ester (DEP) and dipropyl phthalate ester (DPP) were obtained by micellar liquid chromatography (MLC). Experiments were conducted over a temperature range which led to calculation of a Gibbs free energy, enthalpy and entropy of transfer for the phthalate esters. In addition, small angle neutron scattering (SANS) experiments were conducted with no substantial change observed in micelle size before and after phthalate ester incorporation. Overall, a novel method for obtaining thermodynamic information, based on partitioning data, has been developed for dialkyl phthalate esters using micellar liquid chromatography.

Crystal and liquid crystalline polymorphism in 1-alkyl-3-methylimidazolium tetrachloropalladate(II) salts

1-Alkyl-3-methylimidazolium tetrachloropalladate(ii) salts ([C-n-mim](2)[PdCl4], n = 10, 12, 14, 16, 18) containing a single, linear alkyl-chain substituent on the cation have been synthesised and their behaviour characterised by differential scanning calorimetry, polarising optical microscopy and small-angle X-ray scattering. The salts display thermotropic polymorphism, exhibiting both crystal-crystal transitions and, for n = 14-18, the formation of a thermotropic smectic liquid crystalline phase.

Imidazolium ionic liquid crystals with pendant mesogenic groups

Ionic liquid crystals were obtained by coupling one or two mesogenic units (cholesterol or cyanobiphenyl) to an imidazolium cation. Anions are bromide, bis(trifluoromethylsulfonyl)imide, and tetrakis(2-thenoyltrifluoroacetonato)europate(III). The mesomorphism of the compounds depends on the type and number of mesogenic units and on the type of anion. In general, the most stable mesophases are observed for the bis(trifluoromethylsulfonyl)imide salts. Most of the compounds containing cholesterol moieties show enantiotropic SmA* phases over a broad temperature range, and some of them are room temperature liquid crystals. Modeling of the small-angle X-ray scattering patterns revealed the molecular arrangement in these mesophases. On the contrary, most of the compounds containing cyanobiphenyl groups exhibit monotropic lamellar or nematic mesophases, depending on the number of mesogenic units. The imidazolium salts containing the tetrakis(2-thenoyltrifluoroacetonato)europate(III) anion show an intense red photoluminescence.

Thermotropic Ruthenium(II)-Containing Metallomesogens Based on Substituted 1,10-Phenanthroline Ligands

Imidazo[4,5-f]-1,10-phenanthroline and pyrazino[2,3-f]-1,10-phenanthroline substituted with long alkyl chains are versatile ligands for the design of metallomesogens because of the ease of ligand substitution. Whereas the ligands and the corresponding rhenium(I) complexes were not liquid-crystalline, mesomorphism was observed for the corresponding ionic ruthenium(II) complexes with chloride, hexafluorophosphate, and bistriflimide counterions. The mesophases were identified as smectic A phases by high-temperature small-angle X-ray scattering (SAXS) using synchrotron radiation. The transition temperatures depend on the anion, the highest temperatures being observed for the chloride salts and the lowest for the bistriflimide salts. The ruthenium(II) complexes are examples of luminescent ionic liquid crystals.

Selective oxidation of a pyrimidine thioether using supported tantalum catalysts

Ta2O5-SiO2 catalysts were prepared by a sol-gel method using tetraethyl orthosilicate (TEOS) and tantalum (V) ethoxide as the sources of silicon and tantalum, and two families of quaternary ammonium salts, [CnH(2n+1)(CH3)(3)N]Br (n = 14, 16, 18) and [(CnH(2n+1))(4)N]Br (n = 10, 12, 16, 18) as surfactants. The catalysts were compared for the selective suffoxidation of 4,6-dimethyl-2-thiomethylpyrimidine using peroxide as an oxidising agent in a range of ionic liquids and organic solvents. The sol-gel catalysts were also compared with tantalum on MCM-41 prepared by grafting. The catalysts were characterized from adsorption-desorption isotherms of N-2, XRD patterns, small-angle X-ray scattering, IR spectra from adsorbed pyridine and CDCl3, XPS spectra, and Si-29 magic angle spinning (MAS) NNIR experiments. The effect of recycling on the catalyst leaching and selectivity/activity was also studied. High activities and selectivities were found in [NTf2](-) based ionic liquids and organic solvents with good recyclability of the catalyst. Tantalum was found in the solution after reaction; however, this was determined to be due to entrapment of catalyst particulates, as opposed to leaching of the active metal. (c) 2005 Elsevier Inc. All rights reserved.

Thermodynamical studies of irreversible sorption of CO2 by Wyodak coal

Differential scanning calorimetry (DSC), temperature programmed desorption mass spectrometry (TPD-MS) and small angle neutron scattering (SANS) were used to investigate CO2 uptake by the Wyodak coal. The adsorption of carbon dioxide on Wyodak coal was studied by DSC. The exotherms evident at low temperatures are associated with the uptake of CO2 suggesting that carbon dioxide interacts strongly with the coal surface. The reduction in the value of the exotherms between the first and second runs for the Wyodak coal suggests that some CO2 is irreversibly bound to the structure even after heating to 200 °C DSC results also showed that adsorption of CO2 on the coal surface is an activated process and presumably at the temperature of the exotherms there is enough thermal energy to overcome the activation energy for adsorption. The adsorption process is instantly pursued by much slower diffusion of the gas molecules into the coal matrix (absorption). Structural rearrangement in coal by CO2 is examined by change in the glass transition temperature of coal after CO2 uptake at different pressures. The amount of gas dissolved in the coal increases with increasing CO2 pressure. TPD-MS showed that CO2 desorption from the Wyodak coal follows a first order kinetic model. Increase in the activation energy for desorption with pre-adsorbed CO2 pressure suggests that higher pressures facilitate the transport of CO2 molecules through the barriers therefore the amount of CO2 uptake by the coal is greater at higher pressures and more attempts are required to desorb CO2 molecules sorbed at elevated pressures. These conclusions were further confirmed by examining the Wyodak coal structure in high pressure CO 2 by SANS.

Burkholderia cenocepacia BC2L-C Is a Super Lectin with Dual Specificity and Proinflammatory Activity

Lectins and adhesins are involved in bacterial adhesion to host tissues and mucus during early steps of infection. We report the characterization of BC2L-C, a soluble lectin from the opportunistic pathogen Burkholderia cenocepacia, which has two distinct domains with unique specificities and biological activities. The N-terminal domain is a novel TNF-alpha-like fucose-binding lectin, while the C-terminal part is similar to a superfamily of calcium-dependent bacterial lectins. The C-terminal domain displays specificity for mannose and L-glycero-D-manno-heptose. BC2L-C is therefore a superlectin that binds independently to mannose/heptose glycoconjugates and fucosylated human histo-blood group epitopes. The apo form of the C-terminal domain crystallized as a dimer, and calcium and mannose could be docked in the binding site. The whole lectin is hexameric and the overall structure, determined by electron microscopy and small angle X-ray scattering, reveals a flexible arrangement of three mannose/heptose-specific dimers flanked by two fucose-specific TNF-alpha-like trimers. We propose that BC2L-C binds to the bacterial surface in a mannose/heptose-dependent manner via the C-terminal domain. The TNF-alpha-like domain triggers IL-8 production in cultured airway epithelial cells in a carbohydrate-independent manner, and is therefore proposed to play a role in the dysregulated proinflammatory response observed in B. cenocepacia lung infections. The unique architecture of this newly recognized superlectin correlates with multiple functions including bacterial cell cross-linking, adhesion to human epithelia, and stimulation of inflammation.

Structure and dynamics of dextran in binary mixtures of a good and a bad solvent

The structure and dynamics of the common polysaccharide dextran have been investigated in mixed solvents at two different temperatures using small-angle X-ray scattering (SAXS) and viscosity measurements. More specifically, binary mixtures of a good solvent (water, formamide, dimethylsulfoxide, ethanolamine) and the bad solvent ethanol as the minority component have been considered. The experimentally observed effects on the polymer conformation (intrinsic viscosity, coil radius, and radius of gyration) of the bad solvent addition are discussed in terms of hydrogen bonding density and are correlated with the Hansen solubility parameters and the surface tension of the solvent mixtures. Hydrogen bonding appears to be an important contributor to the solubility of dextran but is not sufficient to capture the dextran coil contraction in the mixtures of good+bad solvents.

Fluid Shear Induces Conformation Change in Human Blood Protein von Willebrand Factor in Solution

Many of the physiological functions of von Willebrand Factor (VWF), including its binding interaction with blood platelets, are regulated by the magnitude of applied fluid/hydrodynamic stress. We applied two complementary strategies to study the effect of fluid forces on the solution structure of VWF. First, small-angle neutron scattering was used to measure protein conformation changes in response to laminar shear rates (G) up to 3000/s. Here, purified VWF was sheared in a quartz Couette cell and protein conformation was measured in real time over length scales from 2-140 nm. Second, changes in VWF structure up to 9600/s were quantified by measuring the binding of a fluorescent probe 1,1'-bis(anilino)-4-,4'-bis(naphtalene)-8,8'-disulfonate (bis-ANS) to hydrophobic pockets exposed in the sheared protein. Small angle neutron scattering studies, coupled with quantitative modeling, showed that VWF undergoes structural changes at G < 3000/s. These changes were most prominent at length scales <10 nm (scattering vector (q) range >0.6/nm). A mathematical model attributes these changes to the rearrangement of domain level features within the globular section of the protein. Studies with bis-ANS demonstrated marked increase in bis-ANS binding at G > 2300/s. Together, the data suggest that local rearrangements at the domain level may precede changes at larger-length scales that accompany exposure of protein hydrophobic pockets. Changes in VWF conformation reported here likely regulate protein function in response to fluid shear.

Híbridos orgânicos-inorgânicos para aplicações de baixo custo em óptica integrada

O objectivo desta tese é a utilização de materiais híbridos orgânicos-inorgânicos, designados por di-ureiasis modificados pela adição de tetra-propóxido de zircónio (Zr(i-OPr)4) estabilizado com ácido metacrílico (CH2=C(CH3)COOH), obtidos pela via sol-gel, para aplicações em dispositivos ópticos integrados de baixo custo. A estrutura local dos di-ureiasis com diferentes concentrações de propóxido de zircónio (20 a 80 % mol) foi estudada por difracção de raios-X, espalhamento de raios X a baixos ângulos, microscopia de força atómica, ressonância magnética nuclear dos núcleos dos átomos de 29Si e 13C, espectroscopia no infravermelho por transformada de Fourier, espectroscopia de Raman por transformada de Fourier e termogravimetria. A influência dos parâmetros de síntese, concentração de tetra propóxido de zircónio e rácio tetra propóxido de zircónio: ácido metacrilico na estrutura e propriedades das amostras em monólito e filmes finos (depositados pela técnica de deposição por rotação do substrato) foram avaliadas, permitindo obter amostras transparentes, fotopolimerizáveis e estáveis termicamente até aos 100 ºC. Foram determinadas as propriedades dos guias planares em substratos de vidro borosilicato e silício oxidado (1

Structural Diversity in Antibody Interactions with HIV-1 Env Immunogens

Thesis (Ph.D.)--University of Washington, 2013

Étude structuro-fonctionnelle de SecP43 et caractérisation de ses interactions avec SepSecS et l’ARNtSec in vitro

Selenoproteins are proteins containing selenium in the form of the 21st amino acid, selenocysteine. Selenocysteine (Sec) is directly synthesized onto its cognate tRNA (tRNA[Ser]Sec or tRNASec) and inserted into selenoproteins co-translationally with the help of various cis- and trans-acting factors. Among those factors, SecP43 has been reported to possibly play an essential role in the methylation at the 2’-hydroxylribosyl moiety in the wobble position (Um34) of Sec-tRNA[Ser]Sec and consequently reduce the expression of glutathione peroxidase 1. SecP43 also called tRNASec-associated protein has also been reported to interact in with SepSecS and tRNASec in vivo and the targeted removal of one of these proteins affected the binding of the other to the Sec-tRNASec. The initial aim of the project was to solve the structure of SecP43 by means of x-ray crystallography. Secondly, we were interested in characterizing the interaction of the latter with some of the components of the selenocysteine insertion machinery. These factors are SepSecS and tRNASec. We were able to optimize the expression and the purification of soluble form of the human homologue of SecP43 and of SepSecS by using an adapted auto-induction protocol. This was a major challenge considering that full length SecP43 has not been expressed and purify to date. We did not succeed in crystallizing SecP43. Our failure to crystallize SecP43 is probably due to the fact that it is a partially folded protein as we were able to demonstrate by SAXS (Small Angle X-ray Scattering). The SecP43 envelope calculated by SAXS displayed a rod-shape like structure. In order to enhance the stability of SecP43 required for crystallization, binding affinity studies were conducted to characterize the interaction between SecP43, tRNASec and SepSecS. We did not detect an interaction between SecP43 and tRNASec by using EMSA (Electrophoretic Mobility Shift Assay) and gel filtration. We also could not detect an interaction between SecP43 and SepSecS using a cross-linking assay. In contrast, the tRNASec/SepSecS interaction was demonstrated by EMSA and the addition of SecP43 seemed to reduce the binding affinity. Therefore, SecP43 might induce a conformational change in SepSecS in the presence of tRNASec.