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Organisms living in icy environments produce antifreeze proteins to control ice growth and recrystallization. It has been proposed that these molecules pin the surface of ice crystals, thus inducing the formation of a curved surface that arrests crystal growth. Such proteins are very appealing for many potential applications in food industry, material science and cryoconservation of organs and tissues. Unfortunately, their structural complexity has seriously hampered their practical use, while efficient and accessible synthetic analogues are highly desirable. In this paper, we used molecular dynamics based techniques to model the interaction of three short antifreeze synthetic peptides with an ice surface. The employed protocols succeeded in reproducing the ice pinning action of antifreeze peptides and the consequent ice growth arrest, as well as in distinguishing between antifreeze and control peptides, for which no such effect was observed. Principal components analysis of peptides trajectories in different simulation settings permitted to highlight the main structural features associated to antifreeze activity. Modeling results are highly correlated with experimentally measured properties, and insights on ice-peptide interactions and on conformational patterns favoring antifreeze activity will prompt the design of new and improved antifreeze peptides., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Inc. All rights reserved.)

The solvent effect on the I⋯O halogen bonding in complexes of iodobenzene derivatives with formaldehyde has been investigated by systematically varying the substituents on the iodobenzene ring. Calculations have been performed at MP2 and DFT levels of theory, using the aug-cc-pVDZ basis set and the pseudopotential for iodine. Within the DFT approach, a series of the most widely used exchange-correlation functionals have been considered, comprising PBE, PBE0, B3LYP, BH&HLYP, M06-2X and M06-HF. Results obtained in diethylether and in water using the conductor-like polarizable continuum model (CPCM) have been compared with in vacuo results. Though halogen bonding distances were found to systematically shorten when moving from vacuo to diethylether and then to water, the associated interaction energies showed a decrease in absolute value, indicating that solvent has a destabilizing effect on this interaction. By comparison with MP2 results, all the considered functionals, B3LYP excepted, have been found adequate to describe halogen bonding. As far as the interaction energies are concerned, the best performance was obtained with the M06-HF functional in vacuo and the PBE functional in solution. The geometrical parameters characterizing halogen bonds were better reproduced by the M06-2X functional., (Copyright © 2012 Elsevier Inc. All rights reserved.)

In recent years there is an increased understanding of the molecular conformation of amyloid fibrils. However, much less is known about the early events that lead to the formation of these medically important assemblies. The clarification of these very important mechanistic details on the process may indicate directions towards the inhibition of the early stages of the assembly, where harmful species are most likely to form. Here, we study the dynamics of assembly of short amyloidogenic peptide fragments from the medin polypeptide. This polypeptide is of unique interest since amyloid deposits composed of medin are found almost in all the population above the age of 50. Twelve independent 50 ns long molecular dynamics simulations in explicit water have been run on peptide NH2-NFGSVQFV-COOH, the minimal recognition hexapeptide element, NH2-NFGSVQ-COOH, and several single-point mutants. In all cases a three-stranded polymeric beta-sheet was used as the basic unit from which fibrils can be formed. Our results clearly indicate the need of well-defined sequence and stereochemical constraints to allow the formation of stable well-ordered aggregates. One of the key findings is the need for the presence of a phenylalanine residue, but not other hydrophobic amino acids, in specific positions within the peptide. Taken together, the results are consistent with recent high-resolution structures of amyloid assemblies and provide unique insights into the dynamics of these structures.