Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer

One of the long-term goals in developing advanced biomaterials is to generate protein-like nanostructures and functions from a completely nonnatural polymer. Toward that end, we introduced a high-affinity zinc-binding function into a peptoid (N-substituted glycine polymer) two-helix bundle. Borrowing from well-understood zinc-binding motifs in proteins, thiol and imidazole moieties were positioned within the peptoid such that both helices must align in close proximity to form a binding site. We used fluorescence resonance energy transfer (FRET) reporter groups to measure the change of the distance between the two helical segments and to probe the binding of zinc. We systematically varied the position and number of zinc-binding residues, as well as the sequence and size of the loop that connects the two helical segments. We found that certain peptoid two-helix bundles bind zinc with nanomolar affinities and high selectivity compared to other divalent metal ions. Our work is a significant step toward generating biomimetic nanostructures with enzyme-like functions.     

Photoactive Analogs of Farnesyl Pyrophosphate Containing Benzoylbenzoate Esters: Synthesis and Application to Photoaffinity Labeling of Yeast Protein Farnesyltransferase

Farnesyl pyrophosphate (FPP) is involved in a large number of cellular processes including the prenylation of transforming mutants of Ras proteins implicated in cancer. Photoactive analogs could provide useful information about enzyme active sites that bind farnesyl pyrophosphate; however, the availability of such compounds is extremely limited. Molecules that incorporate benzophenone moieties are attractive photoaffinity labeling reagents because of their useful photochemical properties. Here, the syntheses of two compounds, 3a and 3b, containing para- and meta-substituted benzoylbenzoates are described. Compounds 3a and 3b are competitive inhibitors (with respect to FPP) of yeast protein farnesyltransferase (PFTase) with K(i) values of 910 and 380 nM, respectively. Both compounds inactivate PFTase upon photolysis, resulting in as much as 44% inactivation of enzyme activity. Photolysis of PFTase in the presence of [(32)P]3a or of [(32)P]3b results in preferential labeling of the beta subunit, suggesting that this subunit is involved in prenyl group recognition. These compounds should be valuable tools for studying enzymes that utilize FPP as a substrate.     

Water-barrier properties of mixed bis[trimethoxysilylpropyl]amine and vinyltriacetoxysilane films

X-ray and neutron reflectivity were employed to elucidate the morphologies of bis[trimethoxysilylpropyl]amine silane (A) and vinyltriacetoxysilane (V) mixed films on Si wafers at different A/V ratios, and the response of these films to saturated water vapor. Due to its insensitivity to chemical composition, X-ray reflectivity was used to assess the film density, whereas neutron reflectivity was used to probe water absorption and chemical change on exposure to water. NMR was employed to determine the reaction mechanism in neat AV mixtures and stoichiometry of the initial reaction. X-ray reflectivity reveals about 30% void volume in the films with the least void volume detected near stoichiometry. Grazing incidence small-angle scattering (GISAXS) shows that the void volume is at the molecular level, with no distinct pores. Neutron reflectivity on D2O-conditioned films shows that silane film is not an effective water barrier with about 30 vol % water being absorbed with only a slight thickness increase. Most water is physically absorbed in the void space with the least amount being absorbed near the stoichiometric A/V ratio. The scattering length density of the films almost returns to the virgin state after re-dry following D2O vapor exposure. The film thickness, however, remains at the water-vapor-conditioned state. The slight increase in scattering length density and irreversible thickness change after re-dry indicate some reaction with water during D2O conditioning. A D-rich layer is also observed at the air side surface in D2O-conditioned films regardless of A/V ratio.     

Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding?

The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.     

Finite-size effects on the statistics of extreme events in the BTW model

The BTW Abelian sandpile model is a prominent example of systems showing self-organised criticality (SOC) in the infinite size limit. We study finite-size effects with special focus on the statistics of extreme events, i.e., of particularly large avalanches. Not only the avalanche size probability distribution, but also the mutual independence of large avalanches in the critical state is affected by finite-size effects. Instead of a Poissonian recurrencetime distribution, in the finite system we find a repulsion of extreme events that depends on the avalanche size and not on the respective probability. The dependence of these effects on the system size is investigated and some data collapse is found. Our results imply that SOC is an unsuitable mechanism for the explanation of extreme events which occur in clusters.     

Graphs of difference operators for p-ary sequences

For a given prime p and positive integer n, we consider the graph G _n of the difference operator acting on p-ary sequences of length n. We suggest new proofs of some results of V.I. Arnold on the graph G _n and the complexity of sequences and obtain new results for the length of a maximal cycle in the general case of p-ary sequences. We also provide estimates for the number of complicated sequences.      

A dynamic benchmarking system for assessing the recovery of inpatients: Evidence from the neurorehabilitation process

The shortage of medical resources (mainly beds) is a critical and increasingly prevalent problem affecting hospitals. Of the factors that contribute to these shortages, the ambiguity and insufficiency of the criteria used to identify whether an inpatient should be discharged are among the most detrimental. To address this issue, this study applies data envelopment analysis (DEA) on existing inpatient data from the Neurorehabilitation Center at Toronto’s Bridgepoint Hospital to create a dynamic benchmarking system to evaluate the health stage of an inpatient ready to be discharged. Unlike the more traditional parametric techniques, DEA provides non-subjective benchmarking that does not require any prior specification of the production function making it a more desirable choice for this application. The dynamic model categorizes the inpatient’s discharge status as rejected, under observation, or approved. This new approach not only allows managers to gain insight into the potential causes of medical resource shortages, but also allows clinicians to treat inpatients more effectively based on their discharge categories. For validation, the results of the dynamic model were compared with actual inpatient discharge assessments provided by the Bridgepoint Hospital.     

Detection of hazelnuts and almonds using commercial ELISA test kits

Three commercial sandwich enzyme-linked immunosorbent assay (ELISA) test kits for the detection of hazelnuts and almonds were evaluated. Limits of detection and dynamic ranges were determined for hazelnuts and almonds spiked into cooked oatmeal, dipping chocolate, and muffins (baked). The limit of detection values varied from 1 to 38 μg/g, depending on the food matrix and ELISA test kit. Percent recoveries based on the standards supplied with the test kits varied from 10% to 170%. It is impossible to ascertain whether the percent recoveries reflect the performance of the ELISAs or differences between the protein content of the nuts used to spike the samples and the test kit standards. Unfortunately, reference materials do not exist that can be used to compare the results from different test kits and standardize the test kit standards. Also, insufficient knowledge regarding the epitope specificity of the antibodies used in the ELISAs further hinders interpretation of the results generated by the different test kits.     

The system HCl+InCl3+H2O from 5 to 55°C: Application of Harned's rule

Electromotive-force measurements of cells containing hydrochloric acid and indium chloride have been made to determine the variation of the log of the activity coefficient of hydrochloric acid with change in the amount of indium chloride in the solution. The simpler Harned equations have been used to fit the data. The quadratic terms in the Harned equations for the activity coefficients of HCl in the salt mixtures are required for a good fit of the 968 experimental emf data points at all the experimental ionic strengths and temperatures. The more convenient Pitzer ion-interaction treatment of the data will be reported in a separate publication which will include the values of the Pitzer parameters for pure InCl₃(aq), and mixing parameters for H⁺–In⁺³ and H⁺–In⁺³–Cl^–. A comprehensive investigation on the mixed electrolyte solutions at 11 different constant total ionic strengths ranging from 0.05 to 3.5 mol-kg^–1 was made at 11 temperatures from 5 to 55°C using the cell without liquid junction of the type: Pt,H₂(g, 1 atm)|HCl(m _A)+InCl₃(m _B)+H₂O|AgCl,AG (A).     

Activity Coefficients of Individual Ions from Titration Data

It is shown that the activity coefficients of the anions resulting from the dissociation of a weak polyprotic acid can be obtained from titration data. Activity coefficients are determined in terms of the activity coefficient of the undissociated acid. The extracted activity coefficients are also dependent on the pH scale adopted in the titration process and are considered as operational coefficients. The computational procedure uses an exact equation representing the titration curve and a nonlinear least-squares fitting procedure. As an illustration, the activity coefficients of the anions of succinic acid are determined. The method also allows study of the variation of the activity coefficients with the ionic strength in a straightforward manner.