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Communication: The electrostatic polarization is essential to differentiate the helical propensity in polyalanine mutants.

Research paper by Caiyi C Wei, Dickson D Tung, Yew Mun YM Yip, Ye Y Mei, Dawei D Zhang

Indexed on: 10 May '11Published on: 10 May '11Published in: The Journal of chemical physics



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.