Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential.

ABSTRACT: A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03(2D)), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER03(2D) force field with the implementation of a polarization scheme (AMBER03(2D)p). For comparison, simulations using

SUBMITTER: Gao Y 

PROVIDER: S-EPMC5380191 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature