title: PPII propensity of multiple-guest amino acids in a proline-rich environment.
abstract: There has been considerable debate about the intrinsic PPII propensity of amino acid residues in denatured polypeptides. Experimentally, this scale is based on the behavior of guest amino acid residues placed in the middle of proline-based hosts. We have used classical molecular dynamics simulations combined with replica-exchange methods to carry out a comprehensive analysis of the conformational equilibria of proline-based host oligopeptides with multiple guest amino acids including alanine, glutamine, valine, and asparagine. The tracked structural characteristics include the secondary structural motifs based on the Ramachandran angles and the cis/trans isomerization of the prolyl bonds. In agreement with our recent study of single amino acid guests, we did not observe an intrinsic PPII propensity in any of the guest amino acids in a multiple-guest setting. Instead, the experimental results can be explained in terms of (i) the steric restrictions imposed on the C-terminal guest amino acid that is immediately followed by a proline residue and (ii) an increase in the trans content of the prolyl bonds due to the presence of guest residues. In terms of the latter, we found that the more guests added to the system, the larger the increase in the trans content of the prolyl bonds, which results in an effective increase in the PPII content of the peptide.
authors.affiliation: Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United States.
authors.forename: Mahmoud
authors.initials: M
authors.lastname: Moradi
authors.forename: Volodymyr
authors.initials: V
authors.lastname: Babin
authors.forename: Celeste
authors.initials: C
authors.lastname: Sagui
authors.forename: Christopher
authors.initials: C
authors.lastname: Roland
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry* / Q000235:genetics; D011487:Protein Conformation
chemical_list: D000596:Amino Acids; D010455:Peptides; C011083:polyproline