Search

Study is conducted which focus on calculations and experiments that characterize the nature of sigma-dimers (sigma-P(sub2)) derived from a pair of phenalenyl radicals. Ab initio calculations reveal that the corresponding (one-electron) bond between phenalenyl radical and its closed-shell cation in sigma-P(sub 2)(super +dot) is unstable relative to dissociation.

It has been shown that the results of Q-model coincide very closely with free energy surfaces obtained from large-scale umbrella sampling MD runs on a realistic liquid-state system. The simulations were performed by using shell models for the solute and solvent.

A Golgi and plasma membrane-enriched fraction was isolated from rat brain and incubated at 37 degrees C at pH 7.2 to investigate the breakdown of endogenous amyloid precursor protein (APP). The degradation of APP was accompanied by the concomitant generation of A-beta-containing C-terminal fragments in a time-dependent manner. Findings indicated that a novel Zn2+-dependent metalloprotease activity associated with a Golgi and plasma membrane-enriched fraction can break down endogenous APP to produce A-beta containing C-terminal fragments.

The beta- and gamma-secretases are unidentified endoproteases that cleave the amino- and carboxyl termini, respectively, of the amyloid precursor protein (APP) to yield beta A4 amyloid peptide, the main component of cerebrovascular plaques that cause Alzheimer's disease. A study was conducted to determine if elastase, collagenase or cathepsin D cleaves the carboxyl terminus of APP. The results indicate that an enzyme similar to cathepsin D could be the gamma-secretase.

The role of heparin in regulating [beta]-site amyloid precursor protein cleaving enzyme 1 (BACE1) is clarified by examining the effect of heparin on the activity or recombinant human BACE1 (rBACE1) in vitro. The results have shown that heparin has stimulated the partially active BACE1 zymogen and has provided evidence that heparan sulfate proteoglycams could regulate the rate of A[beta] production in vivo.

The mechanism of transthyretin (TTR) amyloid neurotoxicity on SH-SY5Y neuroblastoma cells is examined. The results reveal that the TTR can bind to the plasma membrane and cause a change in membrane fluidity.

The high symmetry and stability of phenalenyl systems, both as the planar pi-radical and as the pi-cation are desirable characteristics of prototypical aromatic donor/acceptor pairs that encourage their use as (binary) models for the study of intermolecular interactions extant in stacked molecular arrays. The theoretical formulation can correctly account for the experimental enthalpy change in solution of delta Hp=-6.5 kcal mol(super -1) by the inclusion of differential ionic solvation in the formation of the pi-pimer.

Hospital-acquired (nosocomial) infection (HAI) represents a serious threat to public health, both in terms of human casualty and in terms of economic impact On an annual basis, 2 million individuals require prolonged hospitalization, and an estimated 90 000 patients die due to HAI. Economic damages are reported to exceed $4.5 billion, annually. While many disinfectants, including peracetic acid, have been employed to eradicate infectious bacteria, a lack of understanding their mode of action and the corresponding defense mechanisms hinders successful antimicrobial application. We report here the first transcriptome analysis of the response of Pseuclomonas aeruginosa, a pathogen infecting those with cystic fibrosis, upon 20 mm exposure to a sublethal concentration (1 mM) of peracetic acid. As a result, we identified that 570 out of a total of 5570 P. aeruginosa genes showed statistically significant transcript level changes. Our findings indicate that (i) many genes associated with cellular protective processes were induced, (ii) the transcription of genes involved in primary metabolic pathways was repressed, and (iii) the transcription of genes encoding membrane proteins and small molecule transporters was altered. We also observed that genes within operons were highly cotranscribed in this study. Finally, this global transcriptional profile can help identity signature genes that are also activated with other oxidative disinfectants, which may be used to design new more effective treatments or more efficaciously apply existing compounds. [ABSTRACT FROM AUTHOR]

The focus of this work is OS-CCSD-SPT(2), which is a second-order similarity transformed perturbation theory correction to opposite spin coupled cluster singles doubles, where in the latter the same-spin amplitudes are removed and the opposite-spin ones are solved self-consistently. OS-CCSD-SPT(2) is free of empirical parameters, has an instrinsic scaling of O ( N 6 ), and makes no use of triples. We demonstrate that, for non-multireference molecules, OS-CCSD-SPT(2) produces relative energies whose accuracy is significantly higher than what is generally expected of a triples-free model. For example, using PBE0 orbitals in the reference, OS-CCSD-SPT(2) exhibits a mean absolute deviation (MAD) of 1.13 kcal/mol with respect to CCSD(2 F ) benchmark values for the non-multireference subset of W4-08 atomization energies (cf. a MAD > 6.5 kcal/mol for CCSD) and a MAD of 0.68 kcal/mol for the energies of reactions generated from the W4-08 molecules. These MADs are reduced to 0.61 and 0.63 kcal/mol, respectively, by a simple one-parameter spin-component scaling of the OS-CCSD-SPT(2) same-spin correlation energy. OS-CCSD is also naturally amenable to higher order corrections: the associated third-order correction, OS-CCSD-SPT(3), which does involve connected triples and quadruples, exhibits a MAD of 0.44 kcal/mol for the same atomization-energy benchmark.

The effect of dynamic reorganization and confinement of isolated Ti IV catalytic centers supported on silicates is investigated for olefin epoxidation. Active sites consist of grafted single-site calix[4]arene-Ti IV centers or their calcined counterparts. Their location is synthetically controlled to be either unconfined at terminal T-atom positions (denoted as type-(i)) or within confining 12-MR pockets (denoted as type-(ii); diameter ∼7 Å, volume ∼185 Å 3 ) composed of hemispherical cavities on the external surface of zeotypes with *-SVY topology. Electronic structure calculations (density functional theory) indicate that active sites consist of cooperative assemblies of Ti IV centers and silanols. When active sites are located at unconfined type-(i) environments, the rate constants for cyclohexene epoxidation (323 K, 0.05 mM Ti IV , 160 mM cyclohexene, 24 mM tert-butyl hydroperoxide) are 9 ± 2 M -2 s -1 ; whereas within confining type-(ii) 12-MR pockets, there is a ∼5-fold enhancement to 48 ± 8 M -2 s -1 . When a mixture of both environments is initially present in the catalyst resting state, the rate constants reflect confining environments exclusively (40 ± 11 M -2 s -1 ), indicating that dynamic reorganization processes lead to the preferential location of active sites within 12-MR pockets. While activation enthalpies are Δ H ‡ app = 43 ± 1 kJ mol -1 irrespective of active site location, confining environments exhibit diminished entropic barriers (Δ S ‡ app = -68 J mol -1 K -1 for unconfined type-(i) vs -56 J mol -1 K -1 for confining type-(ii)), indicating that confinement leads to more facile association of reactants at active sites to form transition state structures (volume ∼ 225 Å 3 ). These results open new opportunities for controlling reactivity on surfaces through partial confinement on shallow external-surface pockets, which are accessible to molecules that are too bulky to benefit from traditional confinement within micropores.

We demonstrate a block-tensor based implementation of coupled-cluster valence-bond singles and doubles (CCVB-SD) [Small, D. W.; Head-Gordon M. J. Chem. Phys. 2012, 137, 114103] which is a simple modification to restricted CCSD (RCCSD) that provides a qualitatively correct description of valence correlations even in strongly correlated systems. We derive the Λ-equation of CCVB-SD and the corresponding unrelaxed density matrices. The resulting production-level implementation is applied to oligoacenes, correlating up to 318 electrons in 318 orbitals. CCVB-SD shows a qualitative agreement with exact methods for short acenes and reaches the bulk limit of oligoacenes in terms of natural orbital occupation numbers, whereas RCCSD shows nonvariational behavior even for relatively short acenes. A significant reduction in polyradicaloid character is found when correlating all valence electrons instead of only the π-electrons.

We describe an efficient implementation of the coupled cluster valence bond (CCVB) model. CCVB captures a certain essential part of the description of molecules with strong correlations (SC), which allows it to achieve correct energy profiles when covalent bonds are broken, while maintaining proper spin symmetry and size extensivity. To illustrate treatment of SC in bond breaking, we examine the symmetric dissociation of the sulfur allotropes S6 and S8 into triplet S atoms. To show applicability to larger systems and to explore whether CCVB can capture aspects of SC that arise in extended π systems, we report results for a series of acenes up to 12 fused benzene rings, with active spaces of up to 228 correlated electrons. The lowest-energy CCVB solutions found for two of the largest acenes show signatures consistent with multi-electron SC and partial delocalization.

Alzheimer's disease (AD) is a common form of dementia, which is characterized by the presence of extracellular amyloid plaques comprising the amyloid β peptide (Aβ). Although the mechanism underlying AD pathogenesis remains elusive, accumulating evidence suggests that the process of amyloid fibril formation is a surface-mediated event, which plays an important role in AD onset and progression. In this study, the mechanism of Aβ aggregation on hydrophobic surfaces was investigated with dual polarization interferometry (DPI), which provides real-time information on early stages of the aggregation process. Aggregation was monitored on a hydrophobic C18 surface and a polar silicon oxynitride surface. The DPI results showed a characteristic Aβ aggregation pattern involving a decrease in the density of Aβ at the surface followed by an increase in the thickness on the hydrophobic C18 chip. Most importantly, the DPI measurements provided unique information on the early stages of Aβ aggregation, which is characterized by the presence of initially slow nucleus formation process followed by exponential fibril elongation. The dimensions of the putative nucleus corresponded to a thickness of ∼5 nm for both Aβ40 and Aβ42, which may represent about 10-15 molecules. The results thus support the nucleation-dependent polymerization model as indicated by the presence of a nucleation phase followed by an exponential growth phase. These results are the first reported measurements of the real-time changes in Aβ molecular structure during the early stages of amyloid formation at the nanometer level.

Transthyretin (TTR) can deposit as amyloid in the peripheral nervous system and induce a peripheral neuropathy. We examined the mechanism of TTR amyloid neurotoxicity on SH-SY5Y neuroblastoma cells. Wild-type (WT) TTR and two amyloidogenic mutants (V30M and L55P) were expressed in Escherichia coli. Incubation (aging) of WT TTR at 37 degrees C for 1 week caused no significant aggregation. However, there was a significant increase in the extent of amyloid fibril formation after the amyloidogenic mutants had been aged. L55P TTR aggregated more readily than V30M TTR. Both amyloidogenic mutants were neurotoxic after aging. The order of neurotoxicity was as follows: L55P > V30M > WT. As binding of amyloid proteins to the plasma membrane may cause cytotoxicity, we studied the binding of TTR to a plasma membrane-enriched preparation from SH-SY5Y cells by surface plasmon resonance. All three forms bound to the plasma membrane through electrostatic interactions. The binding of the amyloidogenic mutants was increased by aging. The amount of binding correlated closely with the amount of aggregation and with the cytotoxicity of each form. As membrane fluidity can influence cell viability, we also examined the effect of TTR on membrane fluidity using a fluorescence anisotropy method. Binding of the amyloidogenic TTR mutants increased membrane fluidity, and once again, the order of potency was as follows: L55P > V30M > WT. These results demonstrate that TTR can bind to the plasma membrane and cause a change in membrane fluidity. Altered membrane fluidity may be the cause of the neurotoxicity.

Hospital-acquired (nosocomial) infection (HAI) represents a serious threat to public health, both in terms of human casualty and in terms of economic impact. On an annual basis, 2 million individuals require prolonged hospitalization, and an estimated 90 000 patients die due to HAI. Economic damages are reported to exceed $4.5 billion, annually. While many disinfectants, including peracetic acid, have been employed to eradicate infectious bacteria, a lack of understanding their mode of action and the corresponding defense mechanisms hinders successful antimicrobial application. We report here the first transcriptome analysis of the response of Pseudomonas aeruginosa, a pathogen infecting those with cystic fibrosis, upon 20 min exposure to a sublethal concentration (1 mM) of peracetic acid. As a result, we identified that 570 out of a total of 5570 P. aeruginosa genes showed statistically significant transcript level changes. Our findings indicate that (i) many genes associated with cellular protective processes were induced, (ii) the transcription of genes involved in primary metabolic pathways was repressed, and (iii) the transcription of genes encoding membrane proteins and small molecule transporters was altered. We also observed that genes within operons were highly cotranscribed in this study. Finally, this global transcriptional profile can help identify signature genes that are also activated with other oxidative disinfectants, which may be used to design new more effective treatments or more efficaciously apply existing compounds.

We report an enzyme-based method for the in situ entrapment of cells within a biopolymeric hydrogel matrix. Specifically, we used a calcium-independent microbial transglutaminase that is known to cross-link proteins and observed that it catalyzes the formation of gels from a pre-gel solution containing 10% gelatin and E. coli cells. Hydrogel formation occurs 2-3 h after adding transglutaminase, and no additional external intervention is required to initiate gel formation. The in situ entrapped cells grow rapidly and to high cell densities within the gelatin hydrogel. Additionally, the entrapped cells respond to isopropylthiogalactoside induction. The cross-linked gelatin network can be rapidly hydrolyzed (within 1 h) by the protease, proteinase K. Treatment of the network by this protease releases the entrapped E. coli cells. These cells appear unharmed by proteinase K; they can grow and be induced after protease treatment. The ability to in situ entrap, grow, and release cells under mild conditions provides unique opportunities for a range of applications and should be especially useful for microfluidic biosensor systems.