Structural conservation of the short α-helix in modified higher and lower polarity water solutions

Abstract

The three-dimensional structure of a protein defines not only its size and shape, but also its physiological function. It is known that changing the surrounding environment, such as adding an osmolyte or increasing the temperature, could significantly affect the structural and thermodynamic properties of proteins. Therefore, keeping a conserved protein conformation in a specific state is fundamental and very useful for correctly executing the necessary functions. In our present work, the structure change of a single alanine-based ACE-AEAAAKEAAAKA-NH2 peptide in modified polarised water solvents has been investigated by using intensive molecular dynamics simulations. A surprising structural conservation, which is polarity dependent, has been found. When the parameter of polarity S is 0.7 (lower polarity) or 1.2 (higher polarity), the peptide is consistently kept in a folded α-helix state, suggesting the pivotal role of the solvent effect on conformational conservation. In other cases, the peptide mostly exhibits a ringlike structure. The effects of the side chain and salt on the conservation of the peptide’s conformation were explored further and little change was found.