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Origin of the sequence‐dependent polyproline II structure in unfolded peptides
Author(s) -
Kentsis Alex,
Mezei Mihaly,
Osman Roman
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20655
Subject(s) - polyproline helix , chemistry , solvation , side chain , folding (dsp implementation) , intrinsically disordered proteins , protein folding , sequence (biology) , stereochemistry , peptide , biochemistry , solvent , organic chemistry , polymer , electrical engineering , engineering
Recent studies have indicated that the unfolded states of polypeptides contain a substantial amount of polyproline type II (P II ) structure. This energetically and structurally preorganized state may contribute to the reduction of the folding search, as well as to the recognition of intrinsically unstructured proteins and polyproline ligands. Using Monte Carlo simulations of natively unfolded peptides in the presence of explicit aqueous solvation, we observe that residue‐specific P II conformational propensity is the result of the modulation of polypeptide backbone hydration by a proximal side‐chain. Such a mechanism may be unique among those that contribute to the modulation of secondary structures in proteins. The calculated conformational propensities should prove useful for the development of a configurational P II scale necessary for the prediction and design of natural‐like polypeptides. Proteins 2005. © 2005 Wiley‐Liss, Inc.