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.     

A New Series of Aryloxyacetic Acids Endowed with Multi-Target Activity towards Peroxisome Proliferator-Activated Receptors (PPARs), Fatty Acid Amide Hydrolase (FAAH), and Acetylcholinesterase (AChE)

A new series of aryloxyacetic acids was prepared and tested as peroxisome proliferator-activated receptors (PPARs) agonists and fatty acid amide hydrolase (FAAH) inhibitors. Some compounds exhibited an interesting dual activity that has been recently proposed as a new potential therapeutic strategy for the treatment of Alzheimer’s disease (AD). AD is a multifactorial pathology, hence multi-target agents are currently one of the main lines of research for the therapy and prevention of this disease. Given that cholinesterases represent one of the most common targets of recent research, we decided to also evaluate the effects of our compounds on the inhibition of these specific enzymes. Interestingly, two of these compounds, (S)-5 and 6, showed moderate activity against acetylcholinesterase (AChE) and even some activity, although at high concentration, against Aβ peptide aggregation, thus demonstrating, in agreement with the preliminary dockings carried out on the different targets, the feasibility of a simultaneous multi-target activity towards PPARs, FAAH, and AChE. As far as we know, these are the first examples of molecules endowed with this pharmacological profile that might represent a promising line of research for the identification of novel candidates for the treatment of AD.     

The mechanism of Sandmeyer's cyclization reaction by electrospray ionization mass spectrometry

Using electrospray ionization (tandem) mass spectrometry (ESI-MS(/MS)) spectrometric experiments, the Sandmeyer reaction was monitored on-line, and key intermediates were intercepted and characterized for the first time. The mechanistic information provided by on-line ESI-MS(/MS) is in accordance with Sandmeyer's proposal, and was made possible by coupling a microreactor on-line to the ESI ion source, which allowed reactions to be screened from 0.7-2.0 s, identifying and characterizing all intermediates that were formed and consumed during the reaction.     

Delta shock wave for a 3 × 3 hyperbolic system of conservation laws

We study the one-dimensional Riemann problem for a hyperbolic system of three conservation laws of Temple class. The system is a simplification of a recently proposed system of five conservations laws by Bouchut and Boyaval that models viscoelastic fluids. An important issue is that the considered 3×3 system is such that every characteristic field is linearly degenerate. We study theRiemann problemfor this system and under suitable generalized Rankine-Hugoniot relation and entropy condition, both existence and uniqueness of particular delta shock type solutions are established.     

A relativistic quark-diquark model for the nucleon

We developed a constituent quark-diquark model for the nucleon and its resonances using a harmonic oscillator potential for the interaction. The effects due to relativistic kinetic energy correction are studied. Finally, charge form factor of the model is calculated and compared with experimental data.      

Quasi-equilibrium volume changes of polyaniline films upon redox switching. Formal potential distribution and configurational modeling

The quasi-equilibrium electrochemomechanical behavior of relatively thick polyaniline films in sulfuric acid is investigated through experimental measurements and theoretical modeling. The leucoemeraldine (LE)-emeraldine (EM) conversion, or redox switching, is studied. The dependence of film volume and electrochemical charge is determined as a function of applied potential. It is observed that the film volume follows the charge, showing an expansion during the second half of the LE-EM oxidation. The model postulates the existence of a stable intermediate, protoemeraldine (PE), with a formal potential distribution for the PE-EM reaction. The volume change is modeled statistically considering contributions from mixing, polymer deformation, and electrostatic charge. The model shows very good agreement with the experiments, indicating that, in the conditions studied, the deformation contribution dominates the volume changes as a result of the conformational modifications undergone by the polymer in the PE-EM oxidation.     

Particle scattering in loop quantum gravity

We devise a technique for defining and computing -point functions in the context of a background-independent gravitational quantum field theory. We construct a tentative implementation of this technique in a perturbatively finite model defined using spin foam techniques in the context of loop quantum gravity.     

Magnetoelastic instability in molecular antiferromagnetic rings

Lattice stability in a model of an antiferromagnetic ring coupled to adiabatic phonons is investigated for different values of the spin and numbers of magnetic sites. The magnetoelastic transition is shown to be heavily affected by the spin value, displaying a qualitative difference in the nature of the instability for spin one-half. Among the different synthesized materials, Cu8 seems to be the best candidate to observe lattice dimerization in these systems. Our analysis excludes stable lattice distortions in higher spin rings. The effects of thermal fluctuations are studied in the Cu8 model, where a characteristic crossover temperature is estimated.