Physical understanding of complex multiscale biochemical models via algorithmic simplification: Glycolysis in Saccharomyces cerevisiae

Large-scale models of cellular reaction networks are usually highly complex and characterized by a wide spectrum of time scales, making a direct interpretation and understanding of the relevant mechanisms almost impossible. We address this issue by demonstrating the benefits provided by model reduction techniques. We employ the Computational Singular Perturbation (CSP) algorithm to analyze the glycolytic pathway of intact yeast cells in the oscillatory regime. As a primary object of research for many decades, glycolytic oscillations represent a paradigmatic candidate for studying biochemical function and mechanisms. Using a previously published full-scale model of glycolysis, we show that, due to fast dissipative time scales, the solution is asymptotically attracted on a low dimensional manifold. Without any further input from the investigator, CSP clarifies several long-standing questions in the analysis of glycolytic oscillations, such as the origin of the oscillations in the upper part of glycolysis, the importance of energy and redox status, as well as the fact that neither the oscillations nor cell-cell synchronization can be understood in terms of glycolysis as a simple linear chain of sequentially coupled reactions.     

K-sample subsampling in general spaces: The case of independent time series

The problem of subsampling in two-sample and K-sample settings is addressed where both the data and the statistics of interest take values in general spaces. We focus on the case where each sample is a stationary time series, and construct subsampling confidence intervals and hypothesis tests with asymptotic validity. Some examples are also given, and the problem of optimal block size choice is discussed.     

Singlet Oxygen‐Induced Furan Oxidation for Site‐Specific and Chemoselective Peptide Ligation

A novel chemoselective ligation methodology has been developed for the facile construction of peptide‐based fluorescent probes. Furan‐containing peptides were activated by singlet oxygen and covalently engaged by nitrogen nucleophiles to yield stable conjugates. Singlet oxygen was compatible with sensitive amino acid residues within the peptides and a range of fluorophores, bearing different functionalities, were successfully incorporated, illustrating the broad scope of the developed strategy.     

Effect of chirality on the structural behaviour of hydrogen-bonded n-alkylammonium pyroglutamates in the crystalline and smectic state

A set of optically active and racemic n-alkylammonium pyroglutamates from dodecyl to octadecyl were synthesized and characterised. Their thermotropic polymorphism was investigated by polarizing optical microscopy, differential scanning calorimetry and dilatometry. Their structure in the crystalline and smectic state was analysed by X-ray diffraction. The hydrogen bonding of the molecules in the crystalline and smectic layers was examined by infrared spectroscopy. The chirality control over the supramolecular self-assembly of the molecules along with the homochiral and heterochiral architecture of the self-assembled dimers are briefly discussed.     

Structural and magnetic properties of vanadyl dichloride solvates: from molecular units to extended hydrogen-bonded solids

The preparation, structural characterization and magnetic properties of three solvent adducts of VOCl(2), trans-VOCl(2)(THF)(2)(H(2)O) (1), trans-VOCl(2)(H(2)O)(2).2Et(2)O (2) and cis-VOCl(2)(MeOH)(3) (3) are described. In these solids, hydrogen bonding among the inorganic complexes is the critical determinant of the formation of extended magnetic networks. Compound forms one-dimensional double chains where alternating monomers from the two branches of the chain are hydrogen bonded via the V-Cl ... H-O-V network (with an axial water molecule and equatorial chloride ions). Magnetic studies indicate no interaction among the vanadyl centers. The paramagnetism of 1 is consistent with the extension of the network from the hydrogen donor site of the axial water, which is orthogonal to the d(xy) magnetic orbital. Compound 2 forms one-dimensional chains with water molecules of adjacent monomers held together by hydrogen bonds to ether molecules (V-O-H ... O(ether) ... H -O-V). The chain network radiates only through the equatorial plane of the complex where the water molecules are located. The presence of the intervening solvent molecule between hydrogen bonds of the primary coordination sphere magnetically insulates metal centers and compound is also a simple paramagnet. Removal of the solvent turns on the magnetic interaction and neighboring spin centers couple antiferromagnetically. Compound 3 forms a layered structure via V-Cl ... H-O-V hydrogen bonding, where all the hydrogen donor sites participate in the formation of the network. The vanadyl spin centers, at distances of 5.5 and 6.5 A from each other, couple antiferromagnetically (J/k=-0.7 K). Thus, magnetic coupling among metal centers is achieved when the hydrogen bond network directly radiates from the coordination plane containing the magnetic orbital. These results further support the utility of hydrogen bond as a viable design element in the construction of low dimensional, magnetic solids.     

5-Hydroxy-pyrrolone based building blocks as maleimide alternatives for protein bioconjugation and single-site multi-functionalization

Recent dramatic expansion in potential uses of protein conjugates has fueled the development of a wide range of protein modification methods; however, the desirable single-site multi-functionalization of proteins has remained a particularly intransigent challenge. Herein, we present the application of 5-hydroxy-1,5-dihydro-2H-pyrrol-2-ones (5HP2Os) as advantageous alternatives to widely used maleimides for the chemo- and site-selective labeling of cysteine residues within proteins. A variety of 5HP2O building blocks have been synthesized using a one-pot photooxidation reaction starting from simple and readily accessible furans and using visible light and oxygen. These novel reagents display excellent cysteine selectivity and also yield thiol conjugates with superior stability. 5HP2O building blocks offer a unique opportunity to introduce multiple new functionalities into a protein at a single site and in a single step, thus, significantly enhancing the resultant conjugate''s properties.

Recent expansion in potential uses of protein conjugates has fueled the development of a range of protein modification methods; however, the desirable single-site multi-functionalization of proteins has remained a particularly intransigent challenge.     

Amphiphilic hydrogel nanoparticles. Preparation, characterization, and preliminary assessment as new colloidal drug carriers

Inverse emulsion photopolymerization of acrylated poly(ethylene glycol)-bl-poly(propylene glycol)-bl-poly(ethylene glycol) and poly(ethylene glycol) was successfully employed to prepare stable, cross-linked, amphiphilic nanoparticles. Even at low emulsifier concentrations (2%) and high water-to-hexane weight ratios (35/65), the stability of the inverse emulsion allowed for the formation of well-defined colloidal material. Inverse emulsion characteristics and polymerization conditions could be controlled to vary the size of the nanoparticles between 50 and 500 nm. The presence of hydrophobic nanodomains within these otherwise hydrophilic nanoparticles was verified by using pyrene as a microenvironmentally sensitive probe. The hydrophobic poly(propylene glycol)-rich domains appear to be suitable for incorporation of hydrophobic drugs, encapsulating Doxorubicin up to 9.8% (w/w). We believe that the complex nano-architecture of these materials makes them a potentially interesting colloidal drug delivery carrier system and that the method should be useful for a number of amphiphilic macromolecular precursors.     

The O + O2 reaction: quantum detailed probabilities and thermal rate coefficients

The detailed quantum probabilities of the O + O₂ reactive system have been computed at zero total angular momentum using the time-independent quantum program ABC thanks to the restructuring of the code and its implementation on the EGEE production Grid. Their main features are discussed and out of them J-shifting thermal rate coefficients have been computed to compare with the experiment and quasiclassical trajectory results over a wide range of temperatures.     

Synthesis and characterization of model diblock copolymers of poly(dimethylsiloxane) with poly(1,4‐butadiene) or poly(ethylene)

Model diblock copolymers of poly(1,4‐butadiene) (PB) and poly(dimethylsiloxane) (PDMS), PB‐b‐PDMS, were synthesized by the sequential anionic polymerization (high vacuum techniques) of butadiene and hexamethylciclotrisiloxane (D₃) in the presence of sec‐BuLi. By homogeneous hydrogenation of PB‐b‐PDMS, the corresponding poly(ethylene) and poly(dimethylsiloxane) block copolymers, PE‐b‐PDMS, were obtained. The synthesized block copolymers were characterized by nuclear magnetic resonance (¹H and ¹³C NMR), size‐exclusion chromatography (SEC), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), transmission electron microscopy (TEM), and rheology. SEC combined with ¹H NMR analysis indicates that the polydispersity index of the samples (M_w/M_n) is low, and that the chemical composition of the copolymers varies from low to medium PDMS content. According to DSC and TGA experiments, the thermal stability of these block copolymers depends on the PDMS content, whereas TEM analysis reveals ordered arrangements of the microphases. The morphologies observed vary from spherical and cylindrical to lamellar domains. This ordered state (even at high temperatures) was further confirmed by small‐amplitude oscillatory shear flow tests. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1579–1590, 2006