Controllable self-assembly of organic-inorganic amphiphiles containing Dawson polyoxometalate clusters

An organic-inorganic molecular hybrid containing the Dawson polyoxometalate, ((C(4)H(9))(4)N)(5)H[P(2)V(3)W(15)O(59)(OCH(2))(3)CNHCOC(15)H(31)], was synthesized and its surfactant-like amphiphilic properties, represented by the formation of bilayer vesicles, were studied in polar solvents. The vesicle size decreases with both decreasing hybrid concentration and with increasing polarity of the solvent, independently. The self-assembly behavior of this hybrid can be controlled by introducing different counterions into the acetonitrile solutions. The addition of ZnCl(2) and NaI can cause a gradual decrease and increase of vesicular sizes, respectively. Tetraalkylammonium bromide is found to disassemble the vesicle assemblies. Moreover, the original counterions of the hybrid can be replaced with protons, resulting in pH-dependent formation of vesicles in aqueous solutions. The hybrid surfactant can further form micro-needle structures in aqueous solutions upon addition of Ca(2+) ions.     

Polystyrene-poly(ethylene oxide) diblock copolymer: the effect of polystyrene and spreading concentration at the air/water interface

Polystyrene-block-poly(ethylene oxide) (PS-PEO) is an amphiphilic diblock copolymer that undergoes microphase separation when spread at the air/water interface, forming nanosized domains. In this study, we investigate the impact of PS by examining a series of PS-PEO samples containing constant PEO (~17,000 g·mol(-1)) and variable PS (from 3600 to 200,000 g·mol(-1)) through isothermal characterization and atomic force microscopy (AFM). The polymers separated into two categories: predominantly hydrophobic and predominantly hydrophilic with a weight percent of PEO of ~20% providing the boundary between the two. AFM results indicated that predominantly hydrophilic PS-PEO forms dots while more hydrophobic samples yield a mixture of dots and spaghetti with continent-like structures appearing at ~7% PEO or less. These structures reflect a blend of polymer spreading, entanglement, and vitrification as the solvent evaporates. Changing the spreading concentration provides insight into this process with higher concentrations representing earlier kinetic stages and lower concentrations demonstrating later ones. Comparison of isothermal results and AFM analysis shows how polymer behavior at the air/water interface correlates with the observed nanostructures. Understanding the impact of polymer composition and spreading concentration is significant in leading to greater control over the nanostructures obtained through PS-PEO self-assembly and their eventual application as polymer templates.     

Fluxes in "free" and total zinc are essential for progression of intraerythrocytic stages of Plasmodium falciparum

Dynamic fluxes in the concentration of ions and small molecules are fundamental features of cell signaling, differentiation, and development. Similar roles for fluxes in transition metal concentrations are less well established. Here, we show that massive zinc fluxes are essential in the infection cycle of an intracellular eukaryotic parasite. Using single-cell quantitative imaging, we show that growth of the blood-stage Plasmodium falciparum parasite requires acquisition of 30 million zinc atoms per erythrocyte before host cell rupture, corresponding to a 400% increase in total zinc concentration. Zinc accumulates in a freely available form in parasitophorous compartments outside the food vacuole, including mitochondria. Restriction of zinc availability via small molecule treatment causes a drop in mitochondrial membrane potential and severely inhibits parasite growth. Thus, extraordinary zinc acquisition and trafficking are essential for parasite development.     

Deamidation accelerates amyloid formation and alters amylin fiber structure

Deamidation of asparagine and glutamine is the most common nonenzymatic, post-translational modification. Deamidation can influence the structure, stability, folding, and aggregation of proteins and has been proposed to play a role in amyloid formation. However there are no structural studies of the consequences of deamidation on amyloid fibers, in large part because of the difficulty of studying these materials using conventional methods. Here we examine the effects of deamidation on the kinetics of amyloid formation by amylin, the causative agent of type 2 diabetes. We find that deamidation accelerates amyloid formation and the deamidated material is able to seed amyloid formation by unmodified amylin. Using site-specific isotope labeling and two-dimensional infrared (2D IR) spectroscopy, we show that fibers formed by samples that contain deamidated polypeptide contain reduced amounts of β-sheet. Deamidation leads to disruption of the N-terminal β-sheet between Ala-8 and Ala-13, but β-sheet is still retained near Leu-16. The C-terminal sheet is disrupted near Leu-27. Analysis of potential sites of deamidation together with structural models of amylin fibers reveals that deamidation in the N-terminal β-sheet region may be the cause for the disruption of the fiber structure at both the N- and C-terminal β-sheet. Thus, deamidation is a post-translational modification that creates fibers that have an altered structure but can still act as a template for amylin aggregation. Deamidation is very difficult to detect with standard methods used to follow amyloid formation, but isotope-labeled IR spectroscopy provides a means for monitoring sample degradation and investigating the structural consequences of deamidation.     

Atomic origin of hysteresis during cyclic loading of Si due to bond rearrangements at the crack surfaces

The atomistic origin of fatigue failure in micron-sized silicon devices is not fully understood. Two series of density-functional theory calculations on cubic diamond Si explore the effect of surface bond formation on crack healing in systems which exhibit strong surface reconstruction. Both series introduce a separation between Si(100) layers (i.e., the crack) and allow the ions to relax to their minimum-energy configuration. The initial surface ionic positions are either bulk terminated or 2 x 1 reconstructed. A plot of the energy versus the introduced separation reveals that once the surfaces reconstruct, the crack is no longer able to return to the equilibrium configuration. Rather, the healed crack interface contains defects which places the flawed energy minimum at a finite strain of 3% and an increased energy of 1.13 Jm2 relative to the equilibrium configuration. The irreversible plastic deformation supports the mechanism proposed by Kahn et al. [Science 298 1215 (2002)] that invokes mechanically induced subcritical cracking to explain the delayed onset of failure.     

Iron-Catalyzed Halogen Exchange of Trifluoromethyl Arenes**

The facile production of ArCF₂X and ArCX₃ from ArCF₃ using catalytic iron(III)halides is reported, which constitutes the first iron-catalyzed halogen exchange for non-aromatic C−F bonds. Theoretical calculations suggest direct activation of C−F bonds by iron coordination. ArCX₃ and ArCF₂X products of the reaction are synthetically valuable due to their diversification potential. In particular, chloro- and bromodifluoromethyl arenes (ArCF₂Cl, ArCF₂Br respectively) provide access to a myriad of difluoromethyl arene derivatives (ArCF₂R). To optimize for mono-halogen exchange, a statistical method called Design of Experiments was used. Optimized parameters were successfully applied to electron rich and electron deficient aromatic substrates, and to the late stage diversification of flufenoxuron, a commercial insecticide. These methods are highly practical, being run at convenient temperatures and using inexpensive common reagents.     

Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge

Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently, we disclosed the eNTRy rules, a key lesson of which is that the introduction of a primary amine enhances OM permeation in certain contexts. To understand the molecular basis for this finding, we perform an extensive set of molecular dynamics (MD) simulations and free energy calculations comparing the permeation of aminated and amine-free antibiotic derivatives through the most abundant OM porin of E. coli, OmpF. To improve sampling of conformationally flexible drugs in MD simulations, we developed a novel, Monte Carlo and graph theory based algorithm to probe more efficiently the rotational and translational degrees of freedom visited during the permeation of the antibiotic molecule through OmpF. The resulting pathways were then used for free-energy calculations, revealing a lower barrier against the permeation of the aminated compound, substantiating its greater OM permeability. Further analysis revealed that the amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and form favorable electrostatic interactions with specific, highly-conserved charged residues. The importance of these interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, this study provides insights on the importance of the primary amine for antibiotic permeation into Gram-negative pathogens that could help the design of future antibiotics. We also offer a new computational approach for calculating free-energy of processes where relevant molecular conformations cannot be efficiently captured.

A rapid pathway sampling method combining Monte Carlo and graph theory, developed to describe permeation pathways through outer membrane porins, can distinguish between structurally similar analogs with different permeabilities.     

Screening for protease substrate by polyvalent phage display

Proteases are key regulators of many physiological and pathological processes [1,2], and are recognized as important and tractable drug candidates. Consequently, knowledge of protease substrate recognition and specificity promotes identification of biologically relevant substrates, helps elucidating a protease's biological function, and the design of specific inhibitors. Traditional methods for establishing substrate recognition profiles involve the identification of the scissile bond within a given protein substrate by proteomic methods such as Edman degradation. Then, synthetic peptide variants of this sequence can be screened in an iterative fashion to arrive at more optimized substrates. Even though it can be fruitful, this iterative strategy is biased toward the original substrate sequence and it is also tremendously cumbersome. Furthermore, it is not amenable to high throughput analysis. In 1993, Matthew & Wells presented a method for the use of monovalent "substrate phage" libraries for discovering peptide substrates for proteases, in which more than 10(7) potential substrates can be tested concurrently [3]. A library of fusion proteins was constructed containing randomized substrate sequences placed between a binding domain and the gene III coat protein of the filamentous phage, M13, which displays the fusion protein and packages the gene coding for it inside. Each fusion protein was displayed as a single copy on filamentous phagemid particles (substrate phage). This method allows one to rapidly survey the substrate recognition and specificity of individual or closely related members of proteases. Over the past decade, substrate phage screening has shown terrific utility in rapidly determining protease specificity and characterization of substrate recognition profile of proteases. In some cases, the structural insights of the catalytic domain were obtained from comparison of substrate specificity among closely related family of proteases [4-6]. The number of proteases (from various classes) characterized by this approach testifies to its power. Since the initial development of substrate phage library, different versions of the substrate phage cloning vectors have been constructed to further improve the utility of substrate phage display. This review will provide an overview of the construction of substrate phage display libraries, screening of substrate phage libraries, examples of application, summary and future directions.