title: Communication: The electrostatic polarization is essential to differentiate the helical propensity in polyalanine mutants.
abstract: The folding processes of three polyalanine peptides with composition of Ac-(AAXAA)(2)-GY-NH(2) (where X is chosen to be Q, K, and D) are studied by molecular dynamics simulation in solvent of 40% trifluoroethanol using both polarized and unpolarized force fields. The simulations reveal the critical role of polarization effect for quantitative description of helix formation. When polarized force field is used, peptides with distinctive helical propensity are correctly differentiated and the calculated helical contents are in close agreement with experimental measurement, indicating that consideration of polarization effect can correctly predict the effect of sequence variation on helix formation.
authors.affiliation: Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
authors.forename: Caiyi
authors.initials: C
authors.lastname: Wei
authors.forename: Dickson
authors.initials: D
authors.lastname: Tung
authors.forename: Yew Mun
authors.initials: YM
authors.lastname: Yip
authors.forename: Ye
authors.initials: Y
authors.lastname: Mei
authors.forename: Dawei
authors.initials: D
authors.lastname: Zhang
mesh_terms: D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D009154:Mutation; D010455:Peptides / Q000737:chemistry* / Q000235:genetics; D017510:Protein Folding; D017433:Protein Structure, Secondary; D014270:Trifluoroethanol
chemical_list: D010455:Peptides; C019529:polyalanine; D014270:Trifluoroethanol