Inhibition of Cellobiohydrolases from Trichoderma reesei. Synthesis and Evaluation of Some Glucose-, Cellobiose-, and Cellotriose-Derived Hydroximolactams and Imidazoles

The lactam 16 , the hydroximolactams 8 , 20 , 23 , and 27 , and the imidazole 32 were prepared following known methods. They were tested together with the known tetrazole 35 and the hydroximolactams 2 and 36 as inhibitors of the cellobiohydrolases Cel7A and Cel6A from Trichoderma reesei. Cel7A is only weakly inhibited by these compounds. Comparing their inhibitory activity evidences the importance of occupying subsites +1 and +2. The results strongly suggest that the shape of none of the variants of the lactone-type inhibitor motif embodied by these inhibitors is complementary to the subsite −1, i. e., analogous to the transition state. Cel6A is rather strongly inhibited by the cellobiose analogues 20 , 23 , and 32 , and by the cellotriose analogue 27 . Their relative inhibitory activities evidence that binding at subsite −2 depends upon the shape of the moiety occupying subsite −1. There is only a small difference between the inhibition by the hydroximolactams 20 and 23 , which may be (partially) protonated by the catalytic acid of either anti- or syn-protonating glycosidases, and the imidazole 32 , which can only be protonated by anti-protonating glycosidases. The results strongly suggest that shape requirements must be met by glycosidase inhibitors before they can be used to characterize the proton trajectory of glycosidases.     

The promotion of d-type ions during the low energy collision-induced dissociation of some cysteic acid-containing peptides

Low energy collisionally activated dissociations (CAD) of doubly protonated peptides incorporating cysteic acid and arginine residues have been studied. Deuterium labeling experiments have established that loss of the elements of H₂SO₃ occurs with cleavage of one CH bond and transfer of the hydrogen to a neutral fragment. Prominent d-type ions were observed corresponding to cleavage at the cysteic acid residue. The analysis of structural analogs suggested that the unexpectedly low energy requirement for this process is attributable to a charge-proximal process promoted by intra-ionic interaction of the arginine and cysteic acid side chains. CAD (in the collision hexapole of a tandem quadrupole instrument) of electrospray source-formed fragment ions established that the d-type ions can form via b-type ions; there was no evidence of formation via (a _n + 1) or (b _n — H₂SO₃) ions. The equivalent d-ion was observed, albeit with lesser abundance, when the cysteic acid residue was replaced by aspartic acid, but not by glutamic acid.     

Substituent Effect on the Electronic Properties and Morphologies of Self‐Assembling Bisphenazine Derivatives

Tuning electronic properties and morphologies : We report a unique design platform of n‐type organic semiconductors based on asymmetrically substituted bisphenazines that enable tuning of both electronic properties and morphologies of 1D nanostructures (see figure) by using small substituents with various sizes and electronic demands.

     

Minimizing 18O/16O back‐exchange in the relative quantification of ribonucleic acids

The use of isotopically labeled endonuclease digestion products allows for the relative quantification of ribonucleic acids (RNAs). This approach utilizes ribonucleases such as RNase T1 to mediate the incorporation of ¹⁸O onto the 3′‐terminus of the endonuclease digestion product from a solution containing heavy water (H₂¹⁸O). The accuracy and precision of relative quantification are dependent on the efficiency of isotope incorporation and minimizing any possible ¹⁸O to ¹⁶O back‐exchange before or during mass spectral analysis. Here, we have investigated the stability of ¹⁸O‐labeled endonuclease digestion products to back‐exchange. In particular, the effects of pH, temperature and presence of RNase on the back‐exchange process were examined using matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS). We have found that back‐exchange depends on the presence of the RNase—back‐exchange was not observed once the enzyme was removed from the sample. With RNase present, at all pH values examined (from acidic to basic pH), back‐exchange was detected at incubation above room temperature. The rates and extent of back‐exchange were similar at all pH values. In contrast, back‐exchange in the presence of RNase was found to be especially sensitive to incubation temperature—at temperatures below room temperature, minimal back‐exchange was detected. However, back‐exchange increased as the incubation temperature increased. Based on these findings, appropriate sample‐handling and sample storage conditions for isotopically labeled endonuclease digestion products have been identified, and these conditions should improve the accuracy and precision of results from the relative quantification of RNAs obtained by this approach. Copyright © 2009 John Wiley & Sons, Ltd.     

A mathematical model for the first-pass dynamics of antibiotics acting on the cardiovascular system

We present a preliminary first-pass dynamic model for delivery of drug compounds to the lungs and heart. We use a compartmental mass-balance approach to develop a system of nonlinear differential equations for mass accumulated in the heart as a result of intravenous injection. We discuss sensitivity analysis as well as methodology for minimizing mass in the heart while maximizing mass delivered to the lungs on a first circulatory pass.     

Magnetic susceptibility-induced alignment of proteins in reverse micelles

Proteins encapsulated within the aqueous core of reverse micelles are found to partially align in a magnetic field. The degree of alignment is sufficient to result in sizable residual 15N-1H dipolar couplings that can be easily measured. It is found that the magnetic susceptibility of the reverse micelle particle is not dominated by the encapsulated protein. The residual dipolar couplings are found to be structurally meaningful.     

Adsorption behavior of the (+/-)-Tröger's base enantiomers in the phase system of a silica-based packing coated with amylose tri(3,5-dimethyl carbamate) and 2-propanol and molecular modeling interpretation

The binary adsorption isotherms of the enantiomers of Tr?ger's base in the phase system made of Chiral Technologies ChiralPak AD [a silica-based packing coated with amylose tri(3,5-dimethyl carbamate)] as the chiral stationary phase (CSP) and 2-propanol as the mobile phase were measured by the perturbation method. The more retained enantiomer exhibits a S-shaped adsorption isotherm with a clear inflection point, the concentration of the less retained enantiomer having practically no competitive influence on this isotherm: In the entire range of concentrations studied, dq2/dC1 approximately 0. By contrast, the less retained enantiomer has a Langmuir adsorption isotherm when pure. At constant mobile phase concentrations, however, its equilibrium concentration in the adsorbed phase increases with increasing concentration of the more retained enantiomer and dq1/dC2 > 0. This cooperative adsorption behavior, opposed to the classical competitive behavior, is exceedingly rare but was clearly demonstrated in this case. Two adsorption isotherm equations that account for these physical observations were derived. They are based on the formation of an adsorbed multi-layer, as suggested by the isotherm data. The excellent agreement between the experimental overloaded elution profiles of binary mixtures and the profiles calculated with the equilibrium-dispersive model validates this binary isotherm model. The adsorption energies calculated by molecular mechanics (MM) and by molecular dynamics (MD) indicate that the chiral recognition arising from the different interactions between the functional groups of the CSP and the molecules of the Tr?ger's base enantiomers are mainly driven by their Van der Waals interactions. The MD data suggest that the interactions of the (-)-Tr?ger's base with the CSP are more favored by 8+/-(5) kJ/mol than those of (+)-Tr?ger's base. This difference seems to be a contributing factor to the increased retention of the - enantiomer on this chromatographic system. The modeling of the data also indicates that both enantiomers can form high stoichiometry complexes while binding onto the stationary phase, in agreement with the results of the equilibrium isotherm studies.     

Optimisation and characterisation of biosensors based on polyaniline

With lower limits of detection and increased stability constantly being demanded of biosensor devices, characterisation of the constituent layers that make up the sensor has become unavoidable, since this is inextricably linked with its performance. This work describe the optimisation and characterisation of two aspects of sensor performance: a conductive polymer layer (polyaniline) and the immobilised protein layer. The influence of the thickness of polyaniline films deposited electrochemically onto screen-printed electrode surfaces is described in this work in terms of its influence on a variety of amperometric sensor performance characteristics: time to reach steady state, charging current, catalytic current, background current and signal/background ratios. The influence of polymer film thickness on the conductivity and morphology of finished films is also presented.

An electrostatic method of protein immobilisation is used in this work and scanning electron microscopy in conjunction with gold-labelled antibodies and back-scattered electron detection has enabled the direct visualisation of individual groups of proteins on the sensor surface. Such information can provide an insight into the performance of sensors under influence of increasing protein concentrations.     

Chemical oscillations and Turing patterns in a generalized two-variable model of chemical self-replication

Chemical self-replication of oligonucleotides and helical peptides show the so-called square root rate law. Based on this rate we extend our previous work on ideal replicators to include the square root rate and other possible nonlinearities, which we couple with an enzimatic sink. Although the nonlinearity is necessary for complex dynamics, the nature of the sink is the essential feature in the mechanism that allows temporal and spatial patterns. We obtain exact general relations for the Poincare-Adronov-Hopf and Turing bifurcations, and our generalized results include the Higgins, autocatalator, and templator models as specific cases.     

Significant parameters in the optimization of MALDI-TOF-MS for synthetic polymers

One of the most significant issues in any analytical practice is optimization. Optimization and calibration are key factors in quantitation. In matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), instrument optimization is a limitation restricting quantitation. An understanding of the parameters that are most influential and the effects of these parameters on the mass spectrum is required for optimization. This understanding is especially important when characterizing synthetic polymers by MALDI-TOF-MS, due to the breadth of the polymer molecular mass distribution (MMD). Two considerations are important in quantitation, additivity of signal and signal-to-noise (S/N). In this study, the effects of several instrument parameters were studied using an orthogonal experimental design to understand effects on the signal-to-noise (S/N) of a polystyrene distribution. The instrument parameters examined included detector voltage, laser energy, delay time, extraction voltage, and lens voltage. Other parameters considered were polymer concentration and matrix. The results showed detector voltage and delay time were the most influential of the instrument parameters for polystyrene using all trans-retinoic acid (RA) as the matrix. These parameters, as well as laser energy, were most influential for the polystyrene with dithranol as the matrix.