Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

A protocol is described for the treatment of molecular polarization in force field calculations. The resulting model is consistent in that both inter- and intramolecular polarization are handled within a single scheme. An analytical formula for removing intramolecular polarization from a set of atomic multipoles for an arbitrary static structure or conformation is given. With the help of the intramolecular polarization, these permanent atomic multipoles can then be applied in modeling alternative conformations of a molecule. Equipped with this simple technique, one can derive transferable electrostatic parameters for peptides and proteins using flexible model compounds such as dipeptides. The proposed procedure is tested for its ability to describe the electrostatic potential around various configurations of the N-methylacetamide dimer. The effect of different intramolecular polarization schemes on the accuracy of a force field model of the electrostatic potential of alanine dipeptide is investigated. A group-based scheme for including direct intramolecular polarization is shown to be most successful in accounting for the conformational dependence of electrostatic potentials.     

Composition and thermal stability of SiO2-based hybrid materials TEOS-MTEOS system

Hybrid materials with different amounts of organics permanently bound on the inorganic network obtained in the TEOS-MTEOS (tetraethoxysilan-methyltriethoxysilan) system are used for obtaining coatings with different optical and mechanical properties. To study the thermal stability of the mentioned materials, compositions with different molar ratios of the precursors were prepared. The influence of the solvent and water amounts on the gelation process was also investigated. The gels obtained were characterised by IR spectrometry and their decomposition temperatures were determined by DTA/TG. Thermal stability of the gels is rather influenced by their composition than the conditions of the gelation process. This revised version was published online in July 2006 with corrections to the Cover Date.     

Radiation dose contribution from coal-slags used as structural building material

A significant dose contribution on the population could be derived from coal slags used as isolation material. Extremely high natural activities are measured in the coal slag, derived from the region of the settlement Ajka, Hungary. In some buildings monitored, the elevated -doses were nearly 5–10 times higher than the world average ones. The annual average indoor radon concentrations from the slag exceeded 400 Bq/m³ and in some cases up to 1200 Bq/m³. Due to the elevated exposure and the radon concentrations in the dwellings the annual dose was estimated to 8–24 mSv/y more than 5–10 times of the world average one.     

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

A general molecular mechanics (MM) model for treating aqueous Cu²⁺ and Zn²⁺ ions was developed based on valence bond (VB) theory and incorporated into the atomic multipole optimized energetics for biomolecular applications (AMOEBA) polarizable force field. Parameters were obtained by fitting MM energies to that computed by ab initio methods for gas‐phase tetra‐ and hexa‐aqua metal complexes. Molecular dynamics (MD) simulations using the proposed AMOEBA‐VB model were performed for each transition metal ion in aqueous solution, and solvent coordination was evaluated. Results show that the AMOEBA‐VB model generates the correct square‐planar geometry for gas‐phase tetra‐aqua Cu²⁺ complex and improves the accuracy of MM model energetics for a number of ligation geometries when compared to quantum mechanical (QM) computations. On the other hand, both AMOEBA and AMOEBA‐VB generate results for Zn²⁺–water complexes in good agreement with QM calculations. Analyses of the MD trajectories revealed a six‐coordination first solvation shell for both Cu²⁺ and Zn²⁺ ions in aqueous solution, with ligation geometries falling in the range reported by previous studies. © 2012 Wiley Periodicals, Inc.     

CIRCULAR DICHROISM SPECTRA OF SYSTEM I PARTICLES FROM NORMAL CHLOROPLASTS AND CAROTENOID-DEFICIENT MUTANTS OF MAIZE

Abstract— Circular dichroism (CD) spectra were studied in System I particles prepared by digitonin fragmentation of chloroplasts of normal maize and carotenoid-deficient mutants. CD bands of pigment molecules were found to be higher in particles than in solutions. This phenomenon was most pronounced for the particles containing the carotenoid composition of normal chloroplast lamellae. The CD signal of chlorophylls bound to particles of carotenoid-deficient chloroplasts was closer to that found in solutions. This indicates that aggregation and/or binding of chlorophylls in carotenoid-deficient mutants may be less extensive than in normal chloroplasts.     

Development of small molecule inhibitors and probes of human SUMO deconjugating proteases

Sentrin specific proteases (SENPs) are responsible for activating and deconjugating SUMO (Small Ubiquitin like MOdifier) from target proteins. It remains difficult to study this posttranslational modification due to the lack of reagents that can be used to block the removal of SUMO from substrates. Here, we describe the identification of small molecule SENP inhibitors and active site probes containing aza-epoxide and acyloxymethyl ketone (AOMK) reactive groups. Both classes of compounds are effective inhibitors of hSENPs 1, 2, 5, and 7 while only the AOMKs efficiently inhibit hSENP6. Unlike previous reported peptide vinyl sulfones, these compounds covalently labeled the active site cysteine of multiple recombinantly expressed SENP proteases and the AOMK probe showed selective labeling of these SENPs when added to complex protein mixtures. The AOMK compound therefore represents promising new reagents to study the process of SUMO deconjugation.     

Stereochemistry of the hygrolidins

The stereochemistry shown in 6 has been determined by computer modelling for hygrolidin, prototypical member of a new class of macrolide antibiotics.