Catalytic physiological amyloids

Amyloid fibrils have been identified in many protein systems, mostly linked to progression and cytotoxicity in neurodegenerative diseases and other pathologies, but have also been observed in normal physiological systems. A growing body of work has shown that amyloid fibrils can catalyze chemical reactions. Most studies have focused on catalysis by de-novo synthetic amyloid-like peptides; however, recent studies reveal that physiological, native amyloids are catalytic as well. Here, we discuss methodologies and major experimental aspects pertaining to physiological catalytic amyloids. We highlight analyzes of kinetic parameters related to the catalytic activities of amyloid fibrils, structure-function considerations, characterization of the catalytic active sites, and deciphering of catalytic mechanisms.

Accuracy and precision of binding free energy prediction for a tacrine related lead inhibitor of acetylcholinesterase with an arsenal of supercomputerized molecular modelling methods: a comparative study

Nowadays, advanced computational chemistry methods offer various strategies for revealing prospective hit structures in drug development essentially through accurate binding free energy predictions. After the era of molecular docking and quantitative structure-activity relationships, much interest has been lately oriented to perturbed molecular dynamic approaches like replica exchange with solute tempering and free energy perturbation (REST/FEP) and the potential of the mean force with adaptive biasing and accelerated weight histograms (PMF/AWH). Both of these receptor-based techniques can exploit exascale CPU&GPU supercomputers to achieve high throughput performance. In this fundamental study, we have compared the predictive power of a panel of supercomputerized molecular modelling methods to distinguish the major binding modes and the corresponding binding free energies of a promising tacrine related potential antialzheimerics in human acetylcholinesterase. The binding free energies were estimated using flexible molecular docking, molecular mechanics/generalized Born surface area/Poisson-Boltzmann surface area (MM/GBSA/PBSA), transmutation REST/FEP with 12 x 5 ns/λ windows, annihilation FEP with 20 x 5 ns/λ steps, PMF with weight histogram analysis method (WHAM) and 40 x 5 ns samples, and PMF/AWH with 10 x 100 ns replicas. Confrontation of the classical approaches such as canonical molecular dynamics and molecular docking with alchemical calculations and steered molecular dynamics enabled us to show how large errors in ΔG predictions can be expected if these in silico methods are employed in the elucidation of a common case of enzyme inhibition.Communicated by Ramaswamy H. Sarma.

Development of Rapid and High-Precision Colorimetric Device for Organophosphorus Pesticide Detection Based on Microfluidic Mixer Chip

The excessive pesticide residues in cereals, fruit and vegetables is a big threat to human health, and it is necessary to develop a portable, low-cost and high-precision pesticide residue detection scheme to replace the large-scale laboratory testing equipment for rapid detection of pesticide residues. In this study, a colorimetric device for rapid detection of organophosphorus pesticide residues with high precision based on a microfluidic mixer chip was proposed. The microchannel structure with high mixing efficiency was determined by fluid dynamics simulation, while the corresponding microfluidic mixer chip was designed. The microfluidic mixer chip was prepared by a self-developed liquid crystal display (LCD) mask photo-curing machine. The influence of printing parameters on the accuracy of the prepared chip was investigated. The light source with the optimal wavelength of the device was determined by absorption spectrum measurement, and the relationship between the liquid reservoir depth and detection limit was studied by experiments. The correspondence between pesticide concentration and induced voltage was derived. The minimum detection concentration of the device could reach 0.045 mg·L^-1 and the average detection time was reduced to 60 s. The results provide a theoretical and experimental basis for portable and high-precision detection of pesticide residues.