PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure

We present a new software framework for Markov chain Monte Carlo sampling for simulation, prediction, and inference of protein structure. The software package contains implementations of recent advances in Monte Carlo methodology, such as efficient local updates and sampling from probabilistic models of local protein structure. These models form a probabilistic alternative to the widely used fragment and rotamer libraries. Combined with an easily extendible software architecture, this makes PHAISTOS well suited for Bayesian inference of protein structure from sequence and/or experimental data. Currently, two force‐fields are available within the framework: PROFASI and OPLS‐AA/L, the latter including the generalized Born surface area solvent model. A flexible command‐line and configuration‐file interface allows users quickly to set up simulations with the desired configuration. PHAISTOS is released under the GNU General Public License v3.0. Source code and documentation are freely available from http://phaistos.sourceforge.net . The software is implemented in C++ and has been tested on Linux and OSX platforms. © 2013 Wiley Periodicals, Inc.     

Synthesis and characterisation of Fe6 and Fe12 clusters using bicine

Reaction of bicine {BicH₃, N,N-bis(2-hydroxyethyl)glycine} with an Fe(III) oxo-centered pivalate triangle in MeCN in the presence of Et₂NH yields [Et₂NH₂]₂[Fe₆O₂(OH)₂(Bic)₂(O₂CCMe₃)₈], which possesses an S = 5 ground state.Changing the base to NaOMe produces [Fe₁₂O₄(Bic)₄(HBic)₄(O₂CCMe₃)₈], which contains two Fe₆ units bridged by the carboxylate arms from the bicine ligands. The complex displays strong antiferromagnetic coupling leading to an S = 0 ground state.     

Modulation of ligand-field parameters by heme ruffling in cytochromes c revealed by EPR spectroscopy

Electron paramagnetic resonance (EPR) spectra of variants of Hydrogenobacter thermophilus cytochrome c(552) (Ht c-552) and Pseudomonas aeruginosa cytochrome c(551) (Pa c-551) are analyzed to determine the effect of heme ruffling on ligand-field parameters. Mutations introduced at positions 13 and 22 in Ht c-552 were previously demonstrated to influence hydrogen bonding in the proximal heme pocket and to tune reduction potential (E(m)) over a range of 80 mV [Michel, L. V.; Ye, T.; Bowman, S. E. J.; Levin, B. D.; Hahn, M. A.; Russell, B. S.; Elliott, S. J.; Bren, K. L. Biochemistry 2007, 46, 11753-11760]. These mutations are shown here to also increase heme ruffling as E(m) decreases. The primary effect on electronic structure of increasing heme ruffling is found to be a decrease in the axial ligand-field term Δ/λ, which is proposed to arise from an increase in the energy of the d(xy) orbital. Mutations at position 7, previously demonstrated to influence heme ruffling in Pa c-551 and Ht c-552, are utilized to test this correlation between molecular and electronic structure. In conclusion, the structure of the proximal heme pocket of cytochromes c is shown to play a role in determining heme conformation and electronic structure.     

Functional initiators for the ring-opening polymerization of polyesters and polycarbonates: An overview

Functional ring-opening polymerization (ROP) initiators can instill a wide array of chemical, physical, and biological effects into a polymeric chain. Highlighting the versatility of this “active” initiator approach, a broad range of characteristics can be achieved through the use of initiators with chemistries spanning from drugs and dyes (key in the case of drug delivery or nanoparticle applications) through to radically active monomers, polymerization transfer agents, and catalysts. The selection of a suitable “active” initiator (monomers for tandem reactions, dyes, drugs, stereo-catalysts, etc.) can not only provide the final polymers with interesting application potential but also facilitate the implementation of ROP reactions in tandem with other polymerization techniques. Overall, this review will highlight that functionalities and properties can be effectively tuned by exploiting simple chemistry approaches, allowing readers to identify how these approaches could be of benefit to their own work in a range of applications including drug/gene delivery, amphiphilic bio/degradable carriers, drug/scent controlled release, and stereo-controlled polymers.     

The influence of the morphology on the dynamics in ordered diblock copolymer melts

We report on polarized and depolarized dynamic light scattering (DLS) measurements on two asymmetric poly(ethylene‐alt‐propylene‐block‐dimethylsiloxane) (PEP‐PDMS) diblock copolymers in bulk. Apart from the disordered phase, the samples form various ordered morphologies below their respective order‐to‐disorder transition temperatures: One of the samples forms the hexagonal structure composed of PEP cylinders in a PDMS matrix, whereas the other one forms three ordered structures as a function of temperature, among them two cubic micellar structures and a non‐cubic structure. We report here on the dynamic processes found in polarized DLS measurements in the disordered, hexagonal, cubic micellar and non‐cubic structure in the same material.     

Cubic assembly of a geometrically frustrated {Fe12} spin cluster

We describe an S(4)-symmetric {Fe(12)} spin cluster [Fe(12)O(4)(OH)(2)(L)(4)(OAc)(8)][Cl](2) {H(4)L = (HOCH(2)CH(2))(2)NCH(2)CH(2)N(CH(2)CH(2)OH)(2)} where the iron(III) centres describe a squashed hexagonal antiprism. The clusters pack into a large cubic cell with circular cavities, lined by weak C-H···O interactions, and a unit cell volume of over 60,000 ?(3) containing large solvent accessible voids. The core of the cluster is stable in solution, as confirmed by electrospray mass spectrometry. The cluster possesses a non-trivial, frustrated S = 0 ground state, due to the presence of multiple competing antiferromagnetic interactions. The finite temperature Lanczos method has been employed to calculate the temperature dependent magnetic properties of an analogous dodecanuclear S(i) = 3/2 model spin system, in order to reduce the very large Hilbert space. Three archetypal models with two independent exchange coupling parameters have been employed that render a low temperature feature possible, as seen in the χ vs. T plot for the {Fe(12)} spin cluster.     

A method for analysis of dimethyl selenide and dimethyl diselenide by LC-ICP-DRC-MS

The aim of this work was to develop a simple and fast high performance liquid chromatography-inductively coupled argon plasma (ICP) mass spectrometry (MS) method capable of separating and detecting the two volatile selenium species dimethyl selenide (DMeSe) and dimethyl diselenide (DMeDSe) in biological samples. Dimethyl selenide and dimethyl diselenide were separated on a short reversed phase column using an eluent containing 40% methanol and detected by dynamic reaction cell ICP-MS monitoring the (80)Se isotope. The limit of detection was 8 nM for both species (corresponding to 0.6 and 1.3 μg Se/L for DMeDSe and DMeSe, respectively). Both compounds exhibited a linear signal-concentration relationship in the investigated concentration range of 0.1-1 μM with a precision on the determinations better than 3%. The method was applied for analysis of samples from cancer cell lines incubated with methylseleninic acid, selenomethionine, Se-methylselenocysteine, and sodium selenite. DMeDSe were detected in some samples. The method offers a simple and fast analysis of DMeDSe and DMeSe using standard liquid chromatography coupled with ICP-MS equipment and interfacing.     

Stable cation inversion at the MgAl2O4(100) surface

From an interplay of atom-resolved noncontact atomic force microscopy, surface x-ray diffraction experiments, and density functional theory calculations, we reveal the detailed atomic-scale structure of the (100) surface of an insulating ternary metal oxide, MgAl2O4 (spinel). We surprisingly find that the MgAl2O4(100) surface is terminated by an Al and O-rich structure with a thermodynamically favored amount of Al atoms interchanged with Mg. This finding implies that so-called Mg-Al antisites, which are defects in the bulk of MgAl2O4, become a thermodynamically stable and integral part of the surface.