Molecular Dynamics of Lysine Dendrigrafts in Methanol-Water Mixtures

The molecular dynamics method was used to study the structure and properties of dendrigrafts of the first and second generations in methanol-water mixtures with various volume fractions of methanol. At a small volume fraction of methanol, the size and other properties of both dendrigrafts are very similar to those in pure water. A decrease in the dielectric constant of the mixed solvent with an increase in the methanol fraction leads to the penetration of counterions into the dendrigrafts and a reduction of the effective charge. This leads to a gradual collapse of dendrigrafts: a decrease in their size, and an increase in the internal density and the number of intramolecular hydrogen bonds inside them. At the same time, the number of solvent molecules inside the dendrigraft and the number of hydrogen bonds between the dendrigraft and the solvent decrease. At small fractions of methanol in the mixture, the dominant secondary structure in both dendrigrafts is an elongated polyproline II (PPII) helix. At intermediate volume fractions of methanol, the proportion of the PPII helix decreases, while the proportion of another elongated beta-sheet secondary structure gradually increases. However, at a high fraction of methanol, the proportion of compact alpha-helix conformations begins to increase, while the proportion of both elongated conformations decreases.

Automated summary

The molecular dynamics method was used to investigate the structure and properties of dendrigrafts in methanol-water mixtures with varying methanol fractions. At low methanol fractions, the properties of the dendrigrafts resemble those in pure water. With decreasing dielectric constant and increasing methanol fraction, the dendrigrafts experience collapse, resulting in reduced size, increased internal density, and increased intramolecular hydrogen bonds. The secondary structure changes from an elongated polyproline II helix to a beta-sheet structure at intermediate methanol fractions, and eventually transitions to compact alpha-helix conformations at high methanol fractions.