title: Unfolded state of polyalanine is a segmented polyproline II helix.
abstract: Definition of the unfolded state of proteins is essential for understanding their stability and folding on biological timescales. Here, we find that under near physiological conditions the configurational ensemble of the unfolded state of the simplest protein structure, polyalanine alpha-helix, cannot be described by the commonly used Flory random coil model, in which configurational probabilities are derived from conformational preferences of individual residues. We utilize novel effectively ergodic sampling algorithms in the presence of explicit aqueous solvation, and observe water-mediated formation of polyproline II helical (P(II)) structure in the natively unfolded state of polyalanine, and its facilitation of alpha-helix formation in longer peptides. The segmented P(II) helical coil preorganizes the unfolded state ensemble for folding pathway entry by reducing the conformational space available to the diffusive search. Thus, as much as half of the folding search in polyalanine is accomplished by preorganization of the unfolded state.
authors.affiliation: Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, New York, New York 10029, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Kentsis
authors.forename: Mihaly
authors.initials: M
authors.lastname: Mezei
authors.forename: Tatyana
authors.initials: T
authors.lastname: Gindin
authors.forename: Roman
authors.initials: R
authors.lastname: Osman
mesh_terms: D003198:Computer Simulation; D019277:Entropy; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary
chemical_list: D010455:Peptides; C011083:polyproline; C019529:polyalanine