Molecular modeling of butyrylcholinesterase inhibition by cresyl saligenin phosphate

Presumably, aerotoxic syndrome is caused by the impact of tricresyl phosphate (TCP), a lubricating oil additive for aircraft engines, on the human body. The most toxic tri-ortho-isomer of this compound is metabolized in the body to give cresyl saligenin phosphate (CSP), which inhibits butyrylcholinesterase (BChE) giving phosphoserine. In this case, BChE acts as a stoichiometric bioscavenger irreversibly binding CSP and as a biomarker of exposure to low doses of TCP. The mechanism of CSP interaction with BChE at the initial stage of formation of the enzyme—inhibitor complex was studied by molecular modeling techniques. The results indicate that BChE interaction with the (R)-enantiomer of CSP in the most stable envelope conformation of the saligenin ring is most preferable. Comparison of the results obtained using different computation methods demonstrated that the best agreement with experimental data can be achieved by combining standard molecular docking methods with quantum mechanics methods for more accurate structure preparation.     

Modified peptide monolayer binding His-tagged biomolecules for small ligand screening with SPR biosensors

A peptide self-assembled monolayer (SAM) was designed to bind His-tagged biomolecules for surface plasmon resonance (SPR) bioanalysis, which was applied for the determination of K(d) for small ligand screening against CD36. Nonspecific adsorption could be minimized using penta- and hexa-peptide monolayers. In particular, monolayers consisting of 3-mercaptopropionyl-leucinyl-histidinyl-aspartyl-leucinyl-histidinyl-aspartic acid (3-Mpa-LHDLHD) exhibited little (12 ng cm(-2)) nonspecific adsorption in crude serum. Modification of this peptide monolayer with Nα,Nα-bis(carboxymethyl)-L-lysine gave a surface competent for binding His-tagged proteins, as demonstrated using enzyme (human dihydrofolate reductase), protein/antibody and receptor (CD36) examples. Immobilization featured chelation of copper and the His-tagged protein by the peptide monolayer, which could be recycled by removing the copper using imidazole washes prior to reuse.     

Silica nanoparticles containing a rhodamine dye and multiple gold nanorods

Silica shells are grown around colloidally synthesized gold nanorods (AuNRs) to form core–shell particles (AuNR@SiO₂) of variable occupancy, defined as the number of AuNRs per silica particle. Multiple AuNR occupancy within the silica shell, confirmed with high-resolution electron microscopy, is reflected in a redshift of the longitudinal plasmon mode of the nanorods due to multipolar coupling between AuNRs of a favored end–end orientation. In addition to the plasmon resonance that dominates their absorbance spectra, FL-AuNR@SiO₂, core–shell particles incorporating a lipid probe (rhodamine-DOPE), can be monitored by their fluorescence and Raman signals. Optical and scanning electron microscopy (SEM) images are compared directly, enabling the correlation of spectroscopic characteristics with particle morphology. Raman and SEM images show that the most intense Raman signals come from aggregates of AuNRs trapped within the silica matrix. Biexponential fits to fluorescence decays indicate that competing mechanisms of quenching and fluorescence enhancement contribute to a reduced fluorescence lifetime of rhodamine-DOPE located near the AuNRs.     

The Effect of Ring Size on Reactivity: The Diagnostic Value of ‘Rate Profiles’

The rates of cycloalkyl phenyl sulfide formation of a series of homologous bromocycloalkanes upon treatment with sodium benzenethiolate have been determined to ascertain the effect of ring size on reactivity. The ‘rate profile’, i.e., reaction rate vs. ring size, for these nucleophilic substitutions (S_N2) was determined. A linear free‐energy relationship could be derived from computed hydride affinities of cycloalkanes and rates of typical S_N1 reactions, whereas rates of S_N2 reactions exhibited a strong discrepancy from the seven‐ up to the twelve‐membered rings. This discrepancy was rationalized by a careful examination of the geometry of the intermediates and transition states involved in these reactions.     

Isolation and Identification of Two New Fungal Strains for Xylanase Production

Fungi are well known for their ability to excrete enzymes into the environment. The aim of this work was to evaluate xylanase production by fungi isolated from soil. One hundred and thirty-six fungal isolates were screened for xylanase production. Two xylanase producing isolates, FSS117 and FSS129, were identified on the basis of analyses of 5,8S gene sequencing. The closest phylogenetic neighbors according to 5,8S gene sequence data for the two isolates were Aspergillus tubingensis and Aspergillus terreus, respectively. When birchwood xylan or corn cob hulls was used as a substrate for 5 days under submerged culture cultivation, xylanase production from A. terreus FSS129 was 113 and 174 IU ml^?1, respectively. The pH and temperature for optimum xylanase activity were 8 and 65?ºC.     

A branch-and-cut-and-price approach for the pickup and delivery problem with shuttle routes

The Pickup and Delivery Problem with Shuttle routes (PDPS) is a special case of the Pickup and Delivery Problem with Time Windows (PDPTW) where the trips between the pickup points and the delivery points can be decomposed into two legs. The first leg visits only pickup points and ends at some delivery point. The second leg is a direct trip – called a shuttle – between two delivery points. This optimization problem has practical applications in the transportation of people between a large set of pickup points and a restricted set of delivery points.     

Domain decomposition and splitting methods for Mortar mixed finite element approximations to parabolic equations

Summary We introduce in this article a new domain decomposition algorithm for parabolic problems that combines Mortar Mixed Finite Element methods for the space discretization with operator splitting schemes for the time discretization. The main advantage of this method is to be fully parallel. The algorithm is proven to be unconditionally stable and a convergence result in (Δt/h ^1/2) is presented.     

Quantum Hall conductivity in a Landau type model with a realistic geometry

In this paper, we revisit some quantum mechanical aspects related to the quantum Hall effect. We consider a Landau type model, paying a special attention to the experimental and geometrical features of quantum Hall experiments. The resulting formalism is then used to compute explicitely the Hall conductivity from a Kubo formula.