Conformations and free energy landscapes of polyproline peptides.

ABSTRACT: The structure of the proline amino acid allows folded polyproline peptides to exist as both left- (PPII) and right-handed (PPI) helices. We have characterized the free energy landscapes of hexamer, nanomer, and tridecamer polyproline peptides in gas phase and implicit water as well as explicit hexane and 1-propanol for the nanomer. To enhance the sampling provided by regular molecular dynamics, we used the recently developed adaptively biased molecular dynamics method, which describes Landau free energy maps in terms of relevant collective variables. These maps, as a function of the collective variables of handedness, radius of gyration, and three others based on the peptide torsion angle omega, were used to determine the relative stability of the different structures, along with an estima

SUBMITTER: Moradi M 

PROVIDER: S-EPMC2791577 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature