Conformational analysis of lipid molecules by self-organizing maps

The authors have studied the use of the self-organizing map (SOM) in the analysis of lipid conformations produced by atomic-scale molecular dynamics simulations. First, focusing on the methodological aspects, they have systematically studied how the SOM can be employed in the analysis of lipid conformations in a controlled and reliable fashion. For this purpose, they have used a previously reported 50 ns atomistic molecular dynamics simulation of a 1-palmitoyl-2-linoeayl-sn-glycero-3-phosphatidylcholine (PLPC) lipid bilayer and analyzed separately the conformations of the headgroup and the glycerol regions, as well as the diunsaturated fatty acid chain. They have elucidated the effect of training parameters on the quality of the results, as well as the effect of the size of the SOM. It turns out that the main conformational states of each region in the molecule are easily distinguished together with a variety of other typical structural features. As a second topic, the authors applied the SOM to the PLPC data to demonstrate how it can be used in the analysis that goes beyond the standard methods commonly used to study the structure and dynamics of lipid membranes. Overall, the results suggest that the SOM method provides a relatively simple and robust tool for quickly gaining a qualitative understanding of the most important features of the conformations of the system, without a priori knowledge. It seems plausible that the insight given by the SOM could be applied to a variety of biomolecular systems and the design of coarse-grained models for these systems.     

Intracomplex general acid/base catalyzed cleavage of RNA phosphodiester bonds: the leaving group effect

The general acid/base catalyzed cleavage of a number of alkyl esters of uridine-3'- (and -5'-)phosphate has been studied by utilizing a cleaving agent, in which the catalytic moiety (a substituted 1,3,5-triazine) is tethered to an anchoring Zn(II):cyclen moiety. Around pH 7, formation of a strong ternary complex between uracil, Zn(II) and cyclen brings the general acid/base catalyst close to the scissile phosphodiester linkage, resulting in rate acceleration of 1-2 orders of magnitude with the uridine-3'-phosphodiesters. Curiously, no acceleration was observed with their 5'-counterparts. A β(lg) value of -0.7 has been determined for the general acid/base catalyzed cleavage, consistent with a proton transfer to the leaving group in the rate-limiting step.     

Combined depletion and electrostatic forces in polymer-induced membrane adhesion: a theoretical model

We develop a semi-quantitative analytical theory to describe adhesion between two identical planar charged surfaces embedded in a polymer-containing electrolyte solution. Polymer chains are uncharged and differ from the solvent by their lower dielectric permittivity. The solution mimics physiological fluids: It contains 0.1 M of monovalent ions and a small number of divalent cations that form tight bonds with the headgroups of charged lipids. The components have heterogeneous spatial distributions. The model was derived self-consistently by combining: (a) a Poisson-Boltzmann like equation for the charge densities, (b) a continuum mean-field theory for the polymer profile, (c) a solvation energy forcing the ions toward the polymer-poor regions, and (d) surface interactions of polymers and electrolytes. We validated the theory via extensive coarse-grained Molecular Dynamics (MD) simulations. The results confirm our analytical model and reveal interesting details not detected by the theory. At high surface charges, polymer chains are mainly excluded from the gap region, while the concentration of ions increases. The model shows a strong coupling between osmotic forces, surface potential and salting-out effects of the slightly polar polymer chains. It highlights some of the key differences in the behaviour of monomeric and polymeric mixed solvents and their responses to Coulomb interactions. Our main findings are: (a) the onset of long-ranged ion-induced polymer depletion force that increases with surface charge density and (b) a polymer-modified repulsive Coulomb force that increases with surface charge density. Overall, the system exhibits homeostatic behaviour, resulting in robustness against variations in the amount of charges. Applications and extensions of the model are briefly discussed.     

Mass transfer limitation in thermogravimetry of biomass gasification

In order to determine the intrinsic reactivity behavior from thermogravimetry studies, the experimental conditions should be such that the reactions are not mass transfer limited. Biomass char usually has a higher reactivity than coal chars. Therefore, mass transfer limitations may be more problematic when studying biomass char reactivity. Chemical reaction kinetics and mass transfer processes present in thermogravimetry are used for modeling the overall reaction rate for spruce bark CO₂ gasification. Thermogravimetric experiments are carried out between 700 and 900 °C, and the CO₂ concentration is varied between 10 and 90 vol%. The intrinsic activation energy is found to be 120 kJ mol^?1. The transition temperature between regimes I and II is here defined when the fraction apparent to true activation energy equals 0.75. Higher external mass transfer (e.g., by decreasing the diffusion path through the crucible’s freeboard), decreasing the sample amounts, and higher CO₂ partial pressures for the Langmuir–Hinshelwood reaction type increase the transition temperature. The results show that the transition temperature between regimes I and II conditions is approx. 1,030 °C for 90 vol% CO₂.     

The role of MFC/NFC swelling in the rheological behavior and dewatering of high consistency furnishes

The influence of swelling on the rheological and dewatering properties of high consistency nanocellulose based furnishes is considered. Different consistencies of suspensions (1–4 %) and furnishes (5–15 %) were prepared made of two distinctly different grades of nanocellulose containing, micro fibrillated (MFC) and nanofibrillated (NFC) cellulose, and systematic comparison between the rheological and dewatering parameters was conducted. The characterization of the rheological and dewatering properties was performed with a stress controlled rheometer combined with an immobilization cell in parallel plate geometry, as well as with an independent gravimetric dewatering device. The surface charge of nanofibrillated cellulose was found to influence the rheological and dewatering properties of the evaluated suspensions and furnishes due to its impact on swelling and effectively bound water. Due to the complex behavior of the novel materials, the immobilization times were difficult to determine from the changes in the damping factor, as often used for coating colors. Instead, we propose a modified method for determination of immobilization times based on a rheological analysis adopting the rate of change in viscoelastic loss factor over time, d(tan δ = G′′/G′)/dt, describing the critical point(s) in the ratio of the viscous to elastic stress response moduli. With this approach we show that it is possible to characterize immobilization of these materials incorporating the concept of the combined physical interactions of the components and the non-removable bound water, without requiring a direct measure of the nanocellulose surface swelling. Based on the results, we hypothesize that fibrillar swelling impacts the dewatering of MFC and NFC suspensions, and furnishes containing them, by an interfiber pore connectivity blocking/sealing mechanism, which effectively defines the immobilization of the material matrix at the end point of free water extraction caused by the physical blocking imposed by the remaining bound water.     

Synthesis and Characterization of Optical Sol–Gel Adhesive for Military Protective Polycarbonate Resin

Sol–gel adhesive material for isostatic hotpressing lamination process was synthesized using 3-aminopropyltrimethoxysilane (APTES), 3-glycidyloxypropyltrimethoxysilane (GPTS) and methacryloxypropyltrimethoxysilane (MPTS) as precursors. Reaction dynamics between APTES and GPTS was followed on-line with Raman spectroscopy. The lamination process was optimized by varying hotpressing times and pressures at the constant temperature. Mechanical shear strength properties were found to be excellent for studied composition, 25–30 kg/cm² at its best. One possible application of laminated polycarbonate (PC) structure is a soldier helmet visor. Therefore, the ballistic protection properties were tested by shooting with 1.1 gram standard fragment, and determining the v₅₀ velocity value, which corresponds to 50% perforation. The laminated structure gave 5.7% better protection compared with the solid polycarbonate. The laminated components were found to have high optical transparency at the visible wavelengths as well as high environmental stability.     

Biosynthetic Conclusions from the Functional Dissection of Oxygenases for Biosynthesis of Actinorhodin and Related Streptomyces Antibiotics

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Highlights? ActVA-ORF5 is a flavin-dependent monooxygenase required for actinorhodin biosynthesis ? ActVA-ORF5 and its three close homologs were functionally dissected ? ActVA-ORF5 and Gra-21 are bifunctional at C-6/C-8, while Med-7 acts only for C-6 ? AlnT exhibits different regiospecificity for oxidation of tricyclic substrates     

ERKALE—A flexible program package for X‐ray properties of atoms and molecules

ERKALE is a novel software program for computing X‐ray properties, such as ground‐state electron momentum densities, Compton profiles, and core and valence electron excitation spectra of atoms and molecules. The program operates at Hartree–Fock or density‐functional level of theory and supports Gaussian basis sets of arbitrary angular momentum and a wide variety of exchange‐correlation functionals. ERKALE includes modern convergence accelerators such as Broyden and ADIIS and it is suitable for general use, as calculations with thousands of basis functions can routinely be performed on desktop computers. Furthermore, ERKALE is written in an object oriented manner, making the code easy to understand and to extend to new properties while being ideal also for teaching purposes. © 2012 Wiley Periodicals, Inc.     

The Hofmeister anion effect and the growth of polyelectrolyte multilayers

The influence of a variety of counteranions on the properties of polyelectrolyte multilayers deposited by layer-by-layer technique is studied by using ellipsometry and AFM. We found out that in thin dry multilayers (20-90 nm) ofpoly(4-styrenesulfonate) (PSS) and poly(diallyldimethylammonium) (PDADMA), the thickness follows reasonably well the position of the counteranion in the Hofmeister series. The polyelectrolyte-counteranion interaction is studied by means of viscosity measurements of semidilute solutions of PDADMA in the presence of different anions. The dynamic viscosities follow the Hofmeister series of anions and correlate with the thickness of multilayers. Two parameters describing the interaction of ions with water, the Jones-Dole viscosity B coefficient and the hydration entropy, are used to explain the anion effect on the developing multilayer thickness. Reasonably smooth and monotonic functional dependence is observed between the layer thickness and these two parameters.