title: Existence of specific "folds" in polyproline II ensembles of an "unfolded"alanine peptide detected by molecular dynamics.
abstract: Equilibrium ensembles of octaalanine (Ac-Ala8-NHMe) in water, prepared with MD, are analyzed for contributing microstates with an RMSD-based conformational clustering algorithm. The extracted ensemble-averaged properties are in excellent agreement with numerous spectroscopic measurements reported with small alanine model peptides in water. However, the dominantly polyproline II-like ensemble of the peptide is found to be populated with a handful of highly position-specific "folds", including beta-turns, beta-hairpins, and helix nuclei, which could be the "seeds" that initiate proteins along their folding pathways.
authors.affiliation: Department of Chemistry and School of Biosciences and Bioengineering, IIT Bombay, Mumbai-400076, India.
authors.forename: Vibin
authors.initials: V
authors.lastname: Ramakrishnan
authors.forename: Ranjit
authors.initials: R
authors.lastname: Ranbhor
authors.forename: Susheel
authors.initials: S
authors.lastname: Durani
mesh_terms: D004151:Dipeptides / Q000737:chemistry*; D006860:Hydrogen Bonding; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary
chemical_list: D004151:Dipeptides; D010455:Peptides; C011083:polyproline; C019529:polyalanine; C002956:alanylalanine