Folding of α_rβ and ϵβ Reverse Turns; A Nanosecond Molecular Dynamics Simulation of the Hexapeptide MSALNT and the Octapeptide NMSALNTL in Water

Abstract

Folding of the hexapeptide MSALNT and the octapeptide NMSALNTL were investigated using 2.8 ns molecular dynamics (MD) simulations in aqueous solution. In the simulation, the central sequence SALN of the hexapeptide folded rapidly within 200 ps into an α_rβ turn conformation (type VIII conformation) and remained in this conformation for the rest of the trajectory. The sequence SALN of the octapeptide needed 2 ns to fold via ϵβ conformations into a similar conformation. The results join the sequences into a growing group of sequences which have a tendency to form secondary structures and thereby to direct protein folding. The structures of the reverse turn conformations were in accordance with the experimental results (Hakalehto et al., Eur. J. Biochem. 250, 19–29 (1997)). The main driving force of folding seems to be the hydrophobic interaction between the side chains of Ala and Leu at the i+1 and i+2 positions of the β-turn.