Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.     

Vibrational spectrum, ab initio calculations, conformational equilibria and torsional modes of 1,3-dichloropropane

Ab initio calculations are reported for three of four possible conformers of 1,3-dichloropropane. The fourth conformer, with Cs symmetry, has a predicted enthalpy difference of more than 1500 cm(-1) from the most stable conformer from each calculation regardless of the basis set used, so there is little chance of observing it. Thus, there is no evidence in the infrared or Raman spectrum of the presence of a fourth conformer. The order of stability given by the ab initio calculations is C2(GG)>C1(AG)>C2v(AA)>Cs(GG'), where A indicates the anti form for one of the CH2Cl groups and G indicates the gauche conformation for the other CH2Cl group relative to the plane of the carbon atoms. Almost every band observed can be confidently assigned to one or another of the conformers. Many observed bands proved to be of a composite nature, with several nearly coincident vibrations of different conformers contributing to the band contour. Nonetheless, a complete assignment of fundamentals is possible for the most stable C2 conformer, and 5 of the fundamentals of the C2v conformer and 13 those of the C1 conformer can be confidently assigned.     

Synthesis of Organic-Inorganic Hybrid Particles by Sol-Gel Chemistry

The synthesis of ORganically MOdified SILica (ORMOSIL) particles has been carried out using both the hydrolytic and non-hydrolytic sol-gel routes. The hybrid (nano)composites are organically modified with an alkyl or aryl group covalently bonded to silicon. Hybrids have been synthesised in an aqueous sol-gel process by a modified Stöber route, producing spherical nanoparticles with diameters in the range 50–300 nm. The size of the particles can be controlled by control of certain reaction parameters. Smaller ormosil nanoparticles can be synthesised by a base-catalysed emulsion polymerisation route, by varying the type and concentration of surfactant and precursor feed rate. In this case, particles in the size range 3.5–10 nm can be obtained. Hybrids have been synthesised from hyperbranched polyesters by encapsulation in a silica matrix using the hydrolytic sol-gel route. Optimisation of the reaction conditions allows the hybrids to be produced as isolated sub-micron spherical particles. Ormosil particles have also been synthesised using the non-hydrolytic sol-gel route, which may lead to products of different morphologies because of the different polarity of the reaction medium. Different reaction conditions were studied in order to optimise the size and shape of the particles, including choice of solvent, use of surfactants and addition of polystyrene. Dimethylsulfoxide acts as a novel oxygen donor for the catalyst-free formation of colourless silsesquioxanes.     

Developments in suppressor technology for inorganic ion analysis by ion chromatography using conductivity detection

A review is presented detailing the development and use of suppression devices for the conductimetric detection of inorganic ions by ion chromatography (IC). An overview of the general response equation for conductivity detection is also given. Topics of discussion include the role and function of suppressors, the development of early suppressors including packed column and membrane devices from 1975 to 1990 and the subsequent progression towards present day commercially available suppressors and recent innovations. Post-suppression devices for signal enhancement are also discussed.     

In situ analysis of solvents on breath and blood: a selected ion flow tube mass spectrometric study

We report measurements of residual vapour levels of xylenes and trimethylbenzenes, present following a floor re-surfacing procedure, using the technique of selected ion flow tube mass spectrometry (SIFT-MS). A subject exposed to controlled amounts of xylene and mesitylene was monitored by direct breath exhalation over a 4-hour period after exposure to the volatile organic compounds (VOCs) had stopped. The headspace gases above 5 mL blood samples taken over this period were also monitored. The decays of the solvent levels with time were fitted to a two-compartment model with residence times for xylene and mesitylene of 0.37 h and 0.38 h, respectively (compartment one) and 2.5 h and 2.8 h, respectively (compartment two).     

Analyses of Stemona alkaloids in Stemona tuberosa by liquid chromatography/tandem mass spectrometry

Alkaloid profiles in Stemona tuberosa were found to be highly variable. Six Stemona alkaloids isolated from the plant were subjected to on-line high-performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI-MS) and tandem mass spectrometry (MS/MS) analyses. Their fragmentation patterns and products were useful for their characterization. The LC/MS fingerprints of these alkaloids, though variable among samples, could provide an overall characterization of the authenticity and quality of this species and help to differentiate it from S. japonica and S. sessilifolia, as all three species are recognized as genuine sources of the herb Radix Stemonae in the Pharmacopoeia of the People's Republic of China.     

Synthesis of photocleavable poly(methyl methacrylate‐block‐d‐lactide) via atom‐transfer radical polymerization and ring‐opening polymerization

The synthesis and characterization of a photocleavable block copolymer containing an ortho‐nitrobenzyl (ONB) linker between poly(methyl methacrylate) and poly(d ‐lactide) blocks is presented here. The block copolymers were synthesized via atom transfer radical polymerization (ATRP) of MMA followed by ring‐opening polymerization (ROP) of d ‐Lactide and ROP of d ‐lactide followed by ATRP of MMA from a difunctional photoresponsive ONB initiator, respectively. The challenges and limitations during synthesis of the photocleavable block copolymers using the difunctional photoresponsive ONB initiator are discussed. The photocleavage of the copolymers occurs under mild conditions by simple irradiation with 302 nm wavelength UV light (Relative intensity at 7.6 cm: 1500 μW/cm²) for several hours. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 4309–4316