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 a-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 (PII) structure in the natively unfolded state of polyalanine, and its facilitation of a-helix formation in longer peptides. The segmented PII helical coil pre-organizes 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 pre-organization of the unfolded state.