How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP,TP2 and ONEG?

Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) ¹H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.

A protocol for simulating intrinsically disordered peptides in aqueous and hydrophobic solvents is proposed. Results from four force fields are compared with experiment. CHARMM36m performs the best for the simulated IDPs in all environments.     

Supralinearity in nuclear research emulsions

Nuclear emulsions processed in discriminating developers, intended to suppress small latent image sites, exhibit supralinear sensitometric blackness-exposure curves, whose character varies according to developing time, concentration, and composition, yielding hittedness ranging from 1 to 8, singly and in combination. These emulsion-processing combinations display the phenomena called ion-kill (sensitization by the transit of a single charged particle) and gamma- kill (sensitization by the overlap of secondary electron paths, whether from x-rays or from the delta-rays of heavy ions) in radiobiology. Here emulsions are blackened by x-rays when these same plates reveal no electron tracks, or no alpha-particle tracks, or even no fission fragment tracks. The supralinearity of the emulsion response to x-rays, and the consequent suppression of low LET radiations suggest that these materials have the potential to mimic the response of biological systems to particulate radiations of different charge and speed.     

Alkyloxycarbonyl group migration in furanosides

A migration of methyloxycarbonyl group from secondary to primary hydroxyl was observed in furanosides (ribosides and xylosides) under usual desilylation conditions using tetrabutylammonium fluoride. The migration was studied further on several alkyloxycarbonyl furanosides under either basic or acidic conditions. As follows from ¹³C labelling experiments and product distribution, the migration in xylosides, proceeds intramolecularly via six-membered cyclic carbonate, whereas in ribosides, the migration is intermolecular. Acidic conditions prevented the migration in ribosides whereas the migration in xylosides was circumvented under neutral conditions.     

On linear-fractional relations and images of angular operators

For plus-operators in a Banach indefinite space, we consider a linear-fractional relation. The classes of operators with the empty domain of definition for such a relation are described. The sufficient (and necessary, in some meaning) conditions for the chain rule to be valid are given.     

A First-Passage Kinetic Monte Carlo algorithm for complex diffusion–reaction systems

We develop an asynchronous event-driven First-Passage Kinetic Monte Carlo (FPKMC) algorithm for continuous time and space systems involving multiple diffusing and reacting species of spherical particles in two and three dimensions. The FPKMC algorithm presented here is based on the method introduced in Oppelstrup et al. [10] and is implemented in a robust and flexible framework. Unlike standard KMC algorithms such as the n-fold algorithm, FPKMC is most efficient at low densities where it replaces the many small hops needed for reactants to find each other with large first-passage hops sampled from exact time-dependent Green’s functions, without sacrificing accuracy. We describe in detail the key components of the algorithm, including the event-loop and the sampling of first-passage probability distributions, and demonstrate the accuracy of the new method. We apply the FPKMC algorithm to the challenging problem of simulation of long-term irradiation of metals, relevant to the performance and aging of nuclear materials in current and future nuclear power plants. The problem of radiation damage spans many decades of time-scales, from picosecond spikes caused by primary cascades, to years of slow damage annealing and microstructure evolution. Our implementation of the FPKMC algorithm has been able to simulate the irradiation of a metal sample for durations that are orders of magnitude longer than any previous simulations using the standard Object KMC or more recent asynchronous algorithms.     

Interference of Data Transmission in Access and Backbone Networks by High-Power Sensor System

Currently, individual optical fibers are mostly used for each non-data application, which is very inefficient and uneconomical. Sharing a single fiber for multiple applications is a promising solution. However, in the case of a non-data application, the situation is much more complicated compared to data because of special application´s requirements. In laboratory setup, we performed a measurement with a standard G.652D optical fiber for analyzing possible interaction of stable frequency/accurate time transmission, 1.25/10Gbps data transmission (typical bitrates for access point-to-point networks), and high-power sensor signal for different channel spacing and different pulse duration of sensor signal.     

High water‐content thermoresponsive hydrogels via electrostatic macrocrosslinking of cellulose nanofibrils

Atom transfer radical polymerization (ATRP) has been utilized to synthesize tri‐ and star‐block copolymers of poly(di(ethylene glycol)methyl ether methacrylate) (PDEGMA) and quaternized poly(2‐(dimethylamino)ethyl methacrylate) (qPDMAEMA). The block copolymers, all with a minimum of two cationically charged blocks, were sequentially used for electrostatic macrocrosslinking of a dilute dispersion of anionic TEMPO‐oxidized cellulose nanofibrils (CNF, 0.3 wt%), forming free‐standing hydrogels. The cationic block copolymers adsorbed irreversibly to the CNF, enabling the formation of ionically crosslinked hydrogels, with a storage modulus of up to 2.9 kPa. The ability of the block copolymers to adsorb to CNF was confirmed by quartz crystal microbalance with dissipation monitoring (QCM‐D) and infrared spectroscopy (FT‐IR), and the thermoresponsive properties of the hydrogels were investigated by rheological stress and frequency sweep, and gravimetric measurements. This method was shown to be promising for the facile production of thermoresponsive hydrogels based on CNF. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 3415–3424     

Enzymatic oxidation of para-substituted arenes: access to new non-racemic chiral metabolites for synthesis

A series of para-substituted benzene derivatives were subjected to whole-cell fermentation with Escherichia coli JM109 (pDTG601), an organism expressing toluene dioxygenase (TDO). Several compounds proved to be excellent substrates for TDO, including 4-bromo-phenylacetylene, 4-bromobenzaldehyde, 4-bromobenzyl alcohol and 4-bromo-allylbenzene. Some of the first para-functionalized diene diols produced using TDO, are useful substrates for further synthetic manipulations, including their use in the potential synthesis of complex natural products.     

Eigenvalue estimates for Schrödinger operators on metric trees

We consider Schrödinger operators on radial metric trees and prove Lieb–Thirring and Cwikel–Lieb–Rozenblum inequalities for their negative eigenvalues. The validity of these inequalities depends on the volume growth of the tree. We show that the bounds are valid in the endpoint case and reflect the correct order in the weak or strong coupling limit.     

Chemical triple-mutant boxes for quantifying cooperativity in intermolecular interactions

Chemical double-mutant cycles have been used to quantify intermolecular functional-group interactions in H-bonded zipper complexes in chloroform. If the same interaction is measured in zippers of different overall stability, the double-mutant cycles can be combined to produce a triple-mutant box. This construct quantifies cooperativity between the functional group interaction of interest and the other interactions that are used to change the overall stability of the complexes. The sum of two edge-to-face aromatic interactions (-2.9 +/- 0.5 kJ mol-1) is shown to be insensitive to changes of up to 13.7 +/- 0.2 kJ mol-1 in the overall stability of the complex. In principle, enthalpic cooperative effects caused by entropy-enthalpy compensation could perturb the measurement of intermolecular interactions when using the double-mutant cycle approach, but these experiments show that, for this system, the magnitude of the effect lies within the error of the measurements.